{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T14:17:27Z","timestamp":1770301047494,"version":"3.49.0"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T00:00:00Z","timestamp":1767830400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T00:00:00Z","timestamp":1770163200000},"content-version":"vor","delay-in-days":27,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"U.S. Department of Energy, Office of Science, through the Biological and Environmental Research (BER) and the Advanced Scientific Computing Research (ASCR) programs","award":["89233218CNA000001"],"award-info":[{"award-number":["89233218CNA000001"]}]},{"name":"U.S. Department of Energy, Office of Science, through the Biological and Environmental Research (BER) and the Advanced Scientific Computing Research (ASCR) programs","award":["89233218CNA000001"],"award-info":[{"award-number":["89233218CNA000001"]}]},{"name":"U.S. Department of Energy, Office of Science, through the Biological and Environmental Research (BER) and the Advanced Scientific Computing Research (ASCR) programs","award":["89233218CNA000001"],"award-info":[{"award-number":["89233218CNA000001"]}]},{"name":"U.S. Department of Energy, Office of Science, through the Biological and Environmental Research (BER) and the Advanced Scientific Computing Research (ASCR) programs","award":["89233218CNA000001"],"award-info":[{"award-number":["89233218CNA000001"]}]},{"name":"U.S. Department of Energy, Office of Science, through the Biological and Environmental Research (BER) and the Advanced Scientific Computing Research (ASCR) programs","award":["89233218CNA000001"],"award-info":[{"award-number":["89233218CNA000001"]}]},{"name":"U.S. Department of Energy, Office of Science, through the Biological and Environmental Research (BER) and the Advanced Scientific Computing Research (ASCR) programs","award":["89233218CNA000001"],"award-info":[{"award-number":["89233218CNA000001"]}]},{"name":"Los Alamos National Laboratory Directed Research Grant","award":["20210082DR"],"award-info":[{"award-number":["20210082DR"]}]},{"name":"Los Alamos National Laboratory Directed Research Grant","award":["20210082DR"],"award-info":[{"award-number":["20210082DR"]}]},{"name":"Los Alamos National Laboratory Directed Research Grant","award":["20210082DR"],"award-info":[{"award-number":["20210082DR"]}]},{"name":"Los Alamos National Laboratory Directed Research Grant","award":["20210082DR"],"award-info":[{"award-number":["20210082DR"]}]},{"name":"Los Alamos National Laboratory Directed Research Grant","award":["20210082DR"],"award-info":[{"award-number":["20210082DR"]}]},{"name":"Los Alamos National Laboratory Directed Research Grant","award":["20210082DR"],"award-info":[{"award-number":["20210082DR"]}]},{"name":"Los Alamos National Laboratory Directed Research Grant","award":["20210082DR"],"award-info":[{"award-number":["20210082DR"]}]},{"name":"United States, National Institute of Health","award":["R01-HD097665"],"award-info":[{"award-number":["R01-HD097665"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/s12859-025-06361-4","type":"journal-article","created":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T05:44:35Z","timestamp":1767851075000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture"],"prefix":"10.1186","volume":"27","author":[{"given":"David H.","family":"Rogers","sequence":"first","affiliation":[]},{"given":"Cullen","family":"Roth","sequence":"additional","affiliation":[]},{"given":"Cameron","family":"Tauxe","sequence":"additional","affiliation":[]},{"given":"Jeannie T.","family":"Lee","sequence":"additional","affiliation":[]},{"given":"Christina R.","family":"Steadman","sequence":"additional","affiliation":[]},{"given":"Karissa Y.","family":"Sanbonmatsu","sequence":"additional","affiliation":[]},{"given":"Anna","family":"Lappala","sequence":"additional","affiliation":[]},{"given":"Shawn R.","family":"Starkenburg","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2026,1,8]]},"reference":[{"key":"6361_CR1","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/s13072-025-00631-4","volume":"18","author":"V Venu","year":"2025","unstructured":"Venu V, et al. Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency. Epigenetics Chromatin. 2025;18:63. https:\/\/doi.org\/10.1186\/s13072-025-00631-4.","journal-title":"Epigenetics Chromatin"},{"key":"6361_CR2","doi-asserted-by":"publisher","unstructured":"Krumm A, et al. Understanding the 3D genome: emerging impacts on human disease. Seminars in cell & developmental biology. Volume 90. Elsevier; 2019. pp. 62\u201377. https:\/\/doi.org\/10.1016\/j.semcdb.2018.07.004.","DOI":"10.1016\/j.semcdb.2018.07.004"},{"issue":"4","key":"6361_CR3","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/s41577-022-00774-5","volume":"23","author":"S Cuartero","year":"2023","unstructured":"CuarteroS, et al. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol. 2023;23(4):206\u201321. https:\/\/doi.org\/10.1038\/s41577-022-00774-5.","journal-title":"Nat Rev Immunol"},{"issue":"2","key":"6361_CR4","doi-asserted-by":"publisher","first-page":"e202104108","DOI":"10.1083\/jcb.202104108","volume":"221","author":"R San Martin","year":"2021","unstructured":"SanMartin R, et al. Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression. J Cell Biol. 2021;221(2):e202104108. https:\/\/doi.org\/10.1083\/jcb.202104108.","journal-title":"J Cell Biol"},{"issue":"12","key":"6361_CR5","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1038\/s41588-019-0538-8","volume":"51","author":"CP Fulco","year":"2019","unstructured":"FulcoCP, et al. Activity-by-contact model of enhancer\u2013promoter regulation from thousands of CRISPR perturbations. Nat Genet. 2019;51(12):1664\u20139. https:\/\/doi.org\/10.1038\/s41588-019-0538-8.","journal-title":"Nat Genet"},{"issue":"19","key":"6361_CR6","doi-asserted-by":"publisher","first-page":"9470","DOI":"10.1093\/nar\/gks736","volume":"40","author":"B Moindrot","year":"2012","unstructured":"MoindrotB, et al. 3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res. 2012;40(19):9470\u201381. https:\/\/doi.org\/10.1093\/nar\/gks736.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"6361_CR7","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1038\/ng1896","volume":"38","author":"M Simonis","year":"2006","unstructured":"SimonisM, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture\u2013on-chip (4 C). Nat Genet. 2006;38(11):1348\u201354. https:\/\/doi.org\/10.1038\/ng1896.","journal-title":"Nat Genet"},{"key":"6361_CR8","doi-asserted-by":"publisher","unstructured":"Zouari YB, et al. Sailing the Hi-C\u2019s: benefits and remaining challenges in mapping chromatin interactions. Nuclear architecture and dynamics. Elsevier; 2018. pp. 457\u201373. https:\/\/doi.org\/10.1016\/B978-0-12-803480-4.00019-3.","DOI":"10.1016\/B978-0-12-803480-4.00019-3"},{"key":"6361_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-020-02167-0","volume":"21","author":"A Roayaei Ardakany","year":"2020","unstructured":"RoayaeiArdakany A, et al. Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation. Genome Biol. 2020;21:1\u201317. https:\/\/doi.org\/10.1186\/s13059-020-02167-0.","journal-title":"Genome Biol"},{"issue":"10","key":"6361_CR10","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.3390\/genes15101293","volume":"15","author":"D Houchens","year":"2024","unstructured":"HouchensD, et al. CoiTAD: detection of topologically associating domains based on clustering of circular influence features from Hi-C data. Genes. 2024;15(10):1293. https:\/\/doi.org\/10.3390\/genes15101293.","journal-title":"Genes"},{"issue":"1","key":"6361_CR11","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1038\/s42003-024-06389-x","volume":"7","author":"V Venu","year":"2024","unstructured":"VenuV, et al. Multi-omics analysis reveals the dynamic interplay between vero host chromatin structure and function during vaccinia virus infection. Commun Biology. 2024;7(1):721. https:\/\/doi.org\/10.1038\/s42003-024-06389-x.","journal-title":"Commun Biology"},{"issue":"42","key":"6361_CR12","doi-asserted-by":"publisher","first-page":"e2107092118","DOI":"10.1073\/pnas.2107092118","volume":"118","author":"A Lappala","year":"2021","unstructured":"LappalaA, et al. Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome. Proc Natl Acad Sci. 2021;118(42):e2107092118. https:\/\/doi.org\/10.1073\/pnas.2107092118.","journal-title":"Proc Natl Acad Sci"},{"issue":"15","key":"6361_CR13","doi-asserted-by":"publisher","first-page":"1817","DOI":"10.1016\/j.devcel.2022.06.016","volume":"57","author":"L Voortman","year":"2022","unstructured":"VoortmanL, et al. Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Dev Cell. 2022;57(15):1817\u201332. https:\/\/doi.org\/10.1016\/j.devcel.2022.06.016.","journal-title":"Dev Cell"},{"issue":"2","key":"6361_CR14","doi-asserted-by":"publisher","first-page":"btaf030","DOI":"10.1093\/bioinformatics\/btaf030","volume":"41","author":"D Pinchuk","year":"2025","unstructured":"PinchukD, et al. HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting. Bioinformatics. 2025;41(2):btaf030. https:\/\/doi.org\/10.1093\/bioinformatics\/btaf030.","journal-title":"Bioinformatics"},{"issue":"6649","key":"6361_CR15","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.1126\/science.adg3797","volume":"380","author":"Z Liu","year":"2023","unstructured":"LiuZ, et al. Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq. Science. 2023;380(6649):1070\u20136. https:\/\/doi.org\/10.1126\/science.adg3797.","journal-title":"Science"},{"issue":"5","key":"6361_CR16","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1016\/j.gde.2013.06.005","volume":"23","author":"R Krishnakumar","year":"2013","unstructured":"KrishnakumarR, et al. Epigenetics of cellular reprogramming. Curr Opin Genet Dev. 2013;23(5):548\u201355. https:\/\/doi.org\/10.1016\/j.gde.2013.06.005.","journal-title":"Curr Opin Genet Dev"},{"issue":"2","key":"6361_CR17","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/s41576-023-00638-1","volume":"25","author":"Y Zhang","year":"2024","unstructured":"ZhangY, et al. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet. 2024;25(2):123\u201341. https:\/\/doi.org\/10.1038\/s41576-023-00638-1.","journal-title":"Nat Rev Genet"},{"key":"6361_CR18","doi-asserted-by":"publisher","first-page":"103060","DOI":"10.1016\/j.sbi.2025.103060","volume":"92","author":"Z Hou","year":"2025","unstructured":"HouZ, et al. In-cell chromatin structure by Cryo-FIB and Cryo-ET. Curr Opin Struct Biol. 2025;92:103060. https:\/\/doi.org\/10.1016\/j.sbi.2025.103060.","journal-title":"Curr Opin Struct Biol"},{"key":"6361_CR19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12575-019-0094-0","volume":"21","author":"O Oluwadare","year":"2019","unstructured":"OluwadareO, et al. An overview of methods for reconstructing 3-D chromosome and genome structures from Hi-C data. Biol Procedures Online. 2019;21:1\u201320. https:\/\/doi.org\/10.1186\/s12575-019-0094-0.","journal-title":"Biol Procedures Online"},{"issue":"14","key":"6361_CR20","doi-asserted-by":"publisher","first-page":"i145","DOI":"10.1093\/bioinformatics\/btz362","volume":"35","author":"AR Ardakany","year":"2019","unstructured":"Ardakany AR, et al. Selfish: discovery of differential chromatin interactions via a self-similarity measure. Bioinformatics. 2019;35(14):i145\u201353. https:\/\/doi.org\/10.1093\/bioinformatics\/btz362","journal-title":"Bioinformatics"},{"key":"6361_CR21","doi-asserted-by":"publisher","unstructured":"Singhal A, et al. Human coronavirus infection reorganizes spatial genomic architecture in permissive lung cells. Research Square. https:\/\/doi.org\/10.21203\/rs.3.rs-3979539\/v1.","DOI":"10.21203\/rs.3.rs-3979539\/v1"},{"key":"6361_CR22","unstructured":"Merkel D, et al. Docker: lightweight linux containers for consistent development and deployment. Linux j. 2014;239(2):2."},{"issue":"6","key":"6361_CR23","doi-asserted-by":"publisher","first-page":"1894","DOI":"10.1021\/ma501985r","volume":"48","author":"A Lappala","year":"2015","unstructured":"Lappala A, et al. Arrested spinodal decomposition in polymer brush collapsing in poor solvent. Macromolecules. 2015;48(6):1894\u2013900. https:\/\/doi.org\/10.1021\/ma501985r.","journal-title":"Macromolecules"},{"key":"6361_CR24","doi-asserted-by":"publisher","first-page":"108171","DOI":"10.1016\/j.cpc.2021.108171","volume":"271","author":"AP Thompson","year":"2022","unstructured":"ThompsonAP, et al. LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comput Phys Commun. 2022;271:108171. https:\/\/doi.org\/10.1016\/j.cpc.2021.108171.","journal-title":"Comput Phys Commun"},{"key":"6361_CR25","doi-asserted-by":"publisher","unstructured":"Gantikow H et al. Rootless containers with podman for HPC. In: International conference on high performance computing. Springer; 2020. pp. 343\u201354. https:\/\/doi.org\/10.1007\/978-3-030-59851-8_23.","DOI":"10.1007\/978-3-030-59851-8_23"},{"key":"6361_CR26","unstructured":"Priedhorsky R et al. Linux containers for fun and profit in HPC. USENIX Open Access Policy. 2020; p. 12. https:\/\/www.osti.gov\/pages\/biblio\/1398926-linux-containers-fun-profit-hpc."},{"issue":"1","key":"6361_CR27","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","volume":"3","author":"NC Durand","year":"2016","unstructured":"DurandNC, et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 2016;3(1):95\u20138. https:\/\/doi.org\/10.1016\/j.cels.2016.07.002.","journal-title":"Cell Syst"},{"key":"6361_CR28","doi-asserted-by":"publisher","unstructured":"Roth C et al. SLUR (M)-py: a SLURM powered pythonic pipeline for parallel processing of 3D (Epi)genomic profiles. Epigenomics, 17(17), 1233\u201347. https:\/\/doi.org\/10.1080\/17501911.2025.2568368","DOI":"10.1080\/17501911.2025.2568368"},{"issue":"3","key":"6361_CR29","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1093\/imanum\/drs019","volume":"33","author":"PA Knight","year":"2013","unstructured":"KnightPA, et al. A fast algorithm for matrix balancing. IMA J Numer Anal. 2013;33(3):1029\u201347. https:\/\/doi.org\/10.1093\/imanum\/drs019.","journal-title":"IMA J Numer Anal"},{"issue":"2","key":"6361_CR30","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1016\/j.cell.2018.05.007","volume":"174","author":"CY Wang","year":"2018","unstructured":"WangCY, et al. SMCHD1 merges chromosome compartments and assists formation of super-structures on the inactive X. Cell. 2018;174(2):406\u201321. https:\/\/doi.org\/10.1016\/j.cell.2018.05.007.","journal-title":"Cell"},{"issue":"1","key":"6361_CR31","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1093\/nar\/gkw1027","volume":"45","author":"PE Li","year":"2017","unstructured":"LiPE, et al. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Res. 2017;45(1):67\u201380. https:\/\/doi.org\/10.1093\/nar\/gkw1027.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"6361_CR32","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41564-023-01344-8","volume":"8","author":"R Wang","year":"2023","unstructured":"WangR, et al. SARS-CoV-2 restructures host chromatin architecture. Nat Microbiol. 2023;8(4):679\u201394. https:\/\/doi.org\/10.1038\/s41564-023-01344-8.","journal-title":"Nat Microbiol"},{"issue":"37","key":"6361_CR33","doi-asserted-by":"publisher","first-page":"1450","DOI":"10.21105\/joss.01450","volume":"4","author":"C Sullivan","year":"2019","unstructured":"SullivanC, et al. PyVista: 3D plotting and mesh analysis through a streamlined interface for the visualization toolkit (VTK). J Open Source Softw. 2019;4(37):1450. https:\/\/doi.org\/10.21105\/joss.01450.","journal-title":"J Open Source Softw"},{"issue":"2","key":"6361_CR34","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1093\/bib\/bbs029","volume":"14","author":"J Wang","year":"2013","unstructured":"WangJ, et al. A brief introduction to web-based genome browsers. Brief Bioinform. 2013;14(2):131\u201343. https:\/\/doi.org\/10.1093\/bib\/bbs029.","journal-title":"Brief Bioinform"},{"issue":"6","key":"6361_CR35","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1101\/gr.229102","volume":"12","author":"WJ Kent","year":"2002","unstructured":"KentWJ, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996\u20131006. https:\/\/doi.org\/10.1101\/gr.229102.","journal-title":"Genome Res"},{"issue":"2","key":"6361_CR36","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","volume":"14","author":"H Thorvaldsd\u00b4ottir","year":"2013","unstructured":"Thorvaldsd\u00b4ottirH, et al. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178\u201392. https:\/\/doi.org\/10.1093\/bib\/bbs017.","journal-title":"Brief Bioinform"},{"issue":"2","key":"6361_CR37","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1016\/j.cels.2018.01.001","volume":"6","author":"JT Robinson","year":"2018","unstructured":"RobinsonJT, et al. Juicebox.js provides a cloud-based visualization system for Hi-C data. Cell Syst. 2018;6(2):256\u20138. https:\/\/doi.org\/10.1016\/j.cels.2018.01.001.","journal-title":"Cell Syst"},{"issue":"1","key":"6361_CR38","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1186\/s13059-018-1486-1","volume":"19","author":"P Kerpedjiev","year":"2018","unstructured":"KerpedjievP, et al. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19(1):125. https:\/\/doi.org\/10.1186\/s13059-018-1486-1.","journal-title":"Genome Biol"},{"issue":"1","key":"6361_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-025-06176-3","volume":"26","author":"JHM Kwek","year":"2025","unstructured":"KwekJHM, et al. MultiVis.js: a software tool for the visualization of multiway chromatin interactions and SPRITE data. BMC Bioinformatics. 2025;26(1):1\u20139. https:\/\/doi.org\/10.1186\/s12859-025-06176-3.","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"6361_CR40","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1038\/s41592-022-01559-3","volume":"19","author":"X Zhu","year":"2022","unstructured":"ZhuX, et al. Nucleome browser: an integrative and multimodal data navigation platform for 4D nucleome. Nat Methods. 2022;19(8):911\u20133. https:\/\/doi.org\/10.1038\/s41592-022-01559-3.","journal-title":"Nat Methods"},{"issue":"7671","key":"6361_CR41","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/nature23884","volume":"549","author":"J Dekker","year":"2017","unstructured":"DekkerJ, et al. The 4D nucleome project. Nature. 2017;549(7671):219\u201326. https:\/\/doi.org\/10.1038\/nature23884.","journal-title":"Nature"},{"issue":"1","key":"6361_CR42","doi-asserted-by":"publisher","first-page":"2365","DOI":"10.1038\/s41467-022-29697-4","volume":"13","author":"SB Reiff","year":"2022","unstructured":"ReiffSB, et al. The 4D nucleome data portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022;13(1):2365. https:\/\/doi.org\/10.1038\/s41467-022-29697-4.","journal-title":"Nat Commun"},{"issue":"D1","key":"6361_CR43","doi-asserted-by":"publisher","first-page":"D882","DOI":"10.1093\/nar\/gkz1062","volume":"48","author":"Y Luo","year":"2020","unstructured":"LuoY, et al. New developments on the encyclopedia of DNA elements (ENCODE) data portal. Nucleic Acids Res. 2020;48(D1):D882\u20139. https:\/\/doi.org\/10.1093\/nar\/gkz1062.","journal-title":"Nucleic Acids Res"},{"key":"6361_CR44","doi-asserted-by":"crossref","first-page":"W117","DOI":"10.1093\/nar\/gkaa843","volume":"48","author":"J Wolff","year":"2020","unstructured":"Wolff J, et al. Galaxy hicexplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Res (London). 2020;48:W117\u201384.","journal-title":"Nucleic Acids Res (London)"},{"issue":"14","key":"6361_CR45","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, et al. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics. 2009;25(14):1754\u201360.","journal-title":"Bioinformatics"},{"issue":"6588","key":"6361_CR46","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1126\/science.abj6987","volume":"376","author":"S Nurk","year":"2022","unstructured":"Nurk S, et al. The complete sequence of a human genome. Science. 2022;376(6588):44\u201353.","journal-title":"Science"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-025-06361-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06361-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-025-06361-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T11:41:25Z","timestamp":1770205285000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12859-025-06361-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,8]]},"references-count":46,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["6361"],"URL":"https:\/\/doi.org\/10.1186\/s12859-025-06361-4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,8]]},"assertion":[{"value":"24 June 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 December 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 January 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"37"}}