{"id":"https://openalex.org/W7203978343","doi":"https://doi.org/10.64898/2026.08.18.745427","title":"Topology-Based Query Framework for Longitudinal Omics Trajectories","display_name":"Topology-Based Query Framework for Longitudinal Omics Trajectories","publication_year":2026,"publication_date":"2026-08-21","ids":{"openalex":"https://openalex.org/W7203978343","doi":"https://doi.org/10.64898/2026.08.18.745427"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.18.745427","doi":"https://doi.org/10.64898/2026.08.18.745427","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.18.745427","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/21/2026.08.18.745427.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/21/2026.08.18.745427.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057676234","display_name":"Nazanin Zounemat Kermani","orcid":"https://orcid.org/0000-0003-2479-3861","observed_orcids":["https://orcid.org/0000-0003-2479-3861"]},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Nazanin Zounemat-Kermani","raw_affiliation_strings":["Data Science Institute, Department of Computing, Faculty of Engineering, Imperial College London, London, United Kingdom","National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-2479-3861","affiliations":[{"raw_affiliation_string":"Data Science Institute, Department of Computing, Faculty of Engineering, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029987255","display_name":"Matthew Richardson","orcid":"https://orcid.org/0000-0002-5701-234X","observed_orcids":["https://orcid.org/0000-0002-5701-234X"]},"institutions":[{"id":"https://openalex.org/I153648349","display_name":"University of Leicester","ror":"https://ror.org/04h699437","country_code":"GB","type":"education","lineage":["https://openalex.org/I153648349"]},{"id":"https://openalex.org/I4210166781","display_name":"NIHR Leicester Biomedical Research Centre","ror":"https://ror.org/05xqxa525","country_code":"GB","type":"facility","lineage":["https://openalex.org/I143804889","https://openalex.org/I153648349","https://openalex.org/I2802445252","https://openalex.org/I34931013","https://openalex.org/I4210166781"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthew Richardson","raw_affiliation_strings":["The Institute for Lung Health, NIHR Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-5701-234X","affiliations":[{"raw_affiliation_string":"The Institute for Lung Health, NIHR Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, United Kingdom","institution_ids":["https://openalex.org/I153648349","https://openalex.org/I4210166781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010383460","display_name":"Alen Faiz","orcid":"https://orcid.org/0000-0003-1740-3538","observed_orcids":["https://orcid.org/0000-0003-1740-3538"]},"institutions":[{"id":"https://openalex.org/I114017466","display_name":"University of Technology Sydney","ror":"https://ror.org/03f0f6041","country_code":"AU","type":"education","lineage":["https://openalex.org/I114017466"]},{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["AU","NL"],"is_corresponding":false,"raw_author_name":"Alen Faiz","raw_affiliation_strings":["Department of Pathology & Medical Biology, UMCG, Groningen, The Netherlands","Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands","Respiratory Bioinformatics and Molecular Biology (RBMB) Group, The University of Technology Sydney, Ultimo, NSW, Australia"],"raw_orcid":"https://orcid.org/0000-0003-1740-3538","affiliations":[{"raw_affiliation_string":"Department of Pathology & Medical Biology, UMCG, Groningen, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]},{"raw_affiliation_string":"Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]},{"raw_affiliation_string":"Respiratory Bioinformatics and Molecular Biology (RBMB) Group, The University of Technology Sydney, Ultimo, NSW, Australia","institution_ids":["https://openalex.org/I114017466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034019229","display_name":"Simeng Wang","orcid":"https://orcid.org/0000-0003-3446-5204","observed_orcids":["https://orcid.org/0000-0003-3446-5204"]},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Siyao Wang","raw_affiliation_strings":["Data Science Institute, Department of Computing, Faculty of Engineering, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-3446-5204","affiliations":[{"raw_affiliation_string":"Data Science Institute, Department of Computing, Faculty of Engineering, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087500148","display_name":"Jeremy Woods","orcid":"https://orcid.org/0000-0002-1542-8144","observed_orcids":["https://orcid.org/0000-0002-1542-8144"]},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kai Sun","raw_affiliation_strings":["Data Science Institute, Department of Computing, Faculty of Engineering, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-1542-8144","affiliations":[{"raw_affiliation_string":"Data Science Institute, Department of Computing, Faculty of Engineering, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056006900","display_name":"Dragana Vuckovic","orcid":"https://orcid.org/0000-0001-9343-6142","observed_orcids":["https://orcid.org/0000-0001-9343-6142"]},"institutions":[{"id":"https://openalex.org/I4392738229","display_name":"MRC Centre for Environment and Health","ror":"https://ror.org/01vw4c203","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4392738229","https://openalex.org/I47508984","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Dragana Vuckovic","raw_affiliation_strings":["MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-9343-6142","affiliations":[{"raw_affiliation_string":"MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I4392738229","https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000474513","display_name":"Maarten van den Berge","orcid":"https://orcid.org/0000-0002-9336-7340","observed_orcids":["https://orcid.org/0000-0002-9336-7340"]},"institutions":[{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Maarten van den Berge","raw_affiliation_strings":["Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-9336-7340","affiliations":[{"raw_affiliation_string":"Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018590706","display_name":"Anke H. Maitland\u2010van der Zee","orcid":"https://orcid.org/0000-0002-0414-3442","observed_orcids":["https://orcid.org/0000-0002-0414-3442","https://orcid.org/0000-0001-9601-2118"]},"institutions":[{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Anke-Hilse Maitland-van der Zee","raw_affiliation_strings":["Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-0414-3442","affiliations":[{"raw_affiliation_string":"Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085940785","display_name":"Ian Sayers","orcid":"https://orcid.org/0000-0001-5601-5410","observed_orcids":["https://orcid.org/0000-0001-5601-5410"]},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ian Sayers","raw_affiliation_strings":["Centre for Respiratory Research, NIHR Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK"],"raw_orcid":"https://orcid.org/0000-0001-5601-5410","affiliations":[{"raw_affiliation_string":"Centre for Respiratory Research, NIHR Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021316752","display_name":"Sven\u2010Erik Dahl\u00e9n","orcid":"https://orcid.org/0000-0002-4993-4002","observed_orcids":["https://orcid.org/0000-0002-4993-4002"]},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Sven-Erik Dahl\u00e9n","raw_affiliation_strings":["The Centre for Allergy Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-4993-4002","affiliations":[{"raw_affiliation_string":"The Centre for Allergy Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048320859","display_name":"Christopher Edward Brightling","orcid":"https://orcid.org/0000-0002-9345-4903","observed_orcids":["https://orcid.org/0000-0002-9345-4903"]},"institutions":[{"id":"https://openalex.org/I153648349","display_name":"University of Leicester","ror":"https://ror.org/04h699437","country_code":"GB","type":"education","lineage":["https://openalex.org/I153648349"]},{"id":"https://openalex.org/I4210166781","display_name":"NIHR Leicester Biomedical Research Centre","ror":"https://ror.org/05xqxa525","country_code":"GB","type":"facility","lineage":["https://openalex.org/I143804889","https://openalex.org/I153648349","https://openalex.org/I2802445252","https://openalex.org/I34931013","https://openalex.org/I4210166781"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christopher Brightling","raw_affiliation_strings":["The Institute for Lung Health, NIHR Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-9345-4903","affiliations":[{"raw_affiliation_string":"The Institute for Lung Health, NIHR Leicester Biomedical Research Centre - Respiratory, University of Leicester, Leicester, United Kingdom","institution_ids":["https://openalex.org/I153648349","https://openalex.org/I4210166781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009297900","display_name":"Salman Siddiqui","orcid":"https://orcid.org/0000-0003-3770-7870","observed_orcids":["https://orcid.org/0000-0003-3770-7870"]},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Salman Siddiqui","raw_affiliation_strings":["National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-3770-7870","affiliations":[{"raw_affiliation_string":"National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036414874","display_name":"Kian Fan Chung","orcid":"https://orcid.org/0000-0001-7101-1426","observed_orcids":["https://orcid.org/0000-0001-7101-1426"]},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kian Fan Chung","raw_affiliation_strings":["National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-7101-1426","affiliations":[{"raw_affiliation_string":"National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024463990","display_name":"Martijn C. Nawijn","orcid":"https://orcid.org/0000-0003-3372-6521","observed_orcids":["https://orcid.org/0000-0003-3372-6521"]},"institutions":[{"id":"https://openalex.org/I1334415907","display_name":"University Medical Center Groningen","ror":"https://ror.org/03cv38k47","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I1334415907"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Martijn C. Nawijn","raw_affiliation_strings":["Department of Pathology & Medical Biology, UMCG, Groningen, The Netherlands","Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0003-3372-6521","affiliations":[{"raw_affiliation_string":"Department of Pathology & Medical Biology, UMCG, Groningen, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]},{"raw_affiliation_string":"Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands","institution_ids":["https://openalex.org/I1334415907","https://openalex.org/I169381384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091504243","display_name":"Marc Chadeau\u2010Hyam","orcid":"https://orcid.org/0000-0001-8341-5436","observed_orcids":["https://orcid.org/0000-0001-8341-5436"]},"institutions":[{"id":"https://openalex.org/I4392738229","display_name":"MRC Centre for Environment and Health","ror":"https://ror.org/01vw4c203","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4392738229","https://openalex.org/I47508984","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marc Chadeau-Hyam","raw_affiliation_strings":["MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-8341-5436","affiliations":[{"raw_affiliation_string":"MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I4392738229","https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063587197","display_name":"Ian Michael Adcock","orcid":"https://orcid.org/0000-0003-2101-8843","observed_orcids":["https://orcid.org/0000-0003-2101-8843"]},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ian Michael Adcock","raw_affiliation_strings":["National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-2101-8843","affiliations":[{"raw_affiliation_string":"National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5057676234"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.34130001068115234,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.34130001068115234,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.3345000147819519,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.17399999499320984,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/trajectory-clustering","display_name":"trajectory clustering","score":0.7070000171661377},{"id":"https://openalex.org/keywords/temporal-heterogeneity","display_name":"temporal heterogeneity","score":0.6930000185966492},{"id":"https://openalex.org/keywords/corticosteroid-withdrawal","display_name":"corticosteroid withdrawal","score":0.8640000224113464}],"concepts":[{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.8242999911308289},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5665000081062317},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5069000124931335},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44209998846054077},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.41850000619888306},{"id":"https://openalex.org/C2776477805","wikidata":"https://www.wikidata.org/wiki/Q4460773","display_name":"Topological data analysis","level":2,"score":0.41440001130104065},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.37070000171661377},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.37049999833106995},{"id":"https://openalex.org/C90119067","wikidata":"https://www.wikidata.org/wiki/Q43260","display_name":"Polynomial","level":2,"score":0.3553999960422516},{"id":"https://openalex.org/C3020672099","wikidata":"https://www.wikidata.org/wiki/Q857354","display_name":"Longitudinal data","level":2,"score":0.35499998927116394},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3474000096321106},{"id":"https://openalex.org/C27403532","wikidata":"https://www.wikidata.org/wiki/Q5532474","display_name":"Generalized estimating equation","level":2,"score":0.3391999900341034},{"id":"https://openalex.org/C2775936607","wikidata":"https://www.wikidata.org/wiki/Q466845","display_name":"Tracking (education)","level":2,"score":0.33640000224113464},{"id":"https://openalex.org/C191172861","wikidata":"https://www.wikidata.org/wiki/Q7899321","display_name":"Upstream (networking)","level":2,"score":0.3257000148296356},{"id":"https://openalex.org/C16012445","wikidata":"https://www.wikidata.org/wiki/Q1501135","display_name":"Mixed model","level":2,"score":0.3222000002861023},{"id":"https://openalex.org/C15190224","wikidata":"https://www.wikidata.org/wiki/Q1417099","display_name":"Accession number (library science)","level":4,"score":0.3167000114917755},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.3091000020503998},{"id":"https://openalex.org/C64543145","wikidata":"https://www.wikidata.org/wiki/Q162942","display_name":"Intersection (aeronautics)","level":2,"score":0.2976999878883362},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.29649999737739563},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.28540000319480896},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2825999855995178},{"id":"https://openalex.org/C102959455","wikidata":"https://www.wikidata.org/wiki/Q7313954","display_name":"Repeated measures design","level":2,"score":0.2775999903678894},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.27639999985694885},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.27070000767707825},{"id":"https://openalex.org/C2777895361","wikidata":"https://www.wikidata.org/wiki/Q1758614","display_name":"Longitudinal study","level":2,"score":0.2678000032901764},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.26750001311302185},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26010000705718994},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.2572000026702881},{"id":"https://openalex.org/C21080849","wikidata":"https://www.wikidata.org/wiki/Q13611879","display_name":"Data point","level":2,"score":0.25450000166893005}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.18.745427","doi":"https://doi.org/10.64898/2026.08.18.745427","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.18.745427","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/21/2026.08.18.745427.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.18.745427","doi":"https://doi.org/10.64898/2026.08.18.745427","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.18.745427","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/21/2026.08.18.745427.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7203978343.pdf","grobid_xml":"https://content.openalex.org/works/W7203978343.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2991167490","https://openalex.org/W2958039836","https://openalex.org/W4283643833","https://openalex.org/W2409777801","https://openalex.org/W2672044520","https://openalex.org/W6906540217","https://openalex.org/W7030220681","https://openalex.org/W7211887784","https://openalex.org/W2996051589","https://openalex.org/W4412069649"],"abstract_inverted_index":{"1":[0],"Abstract":[1],"1.1":[2],"Background":[3],"Many":[4],"longitudinal":[5,70,221,323,329],"omics":[6,71,324],"studies":[7],"contain":[8],"only":[9],"a":[10,40,132,140,252,311],"small":[11],"number":[12],"of":[13,43,68,78,104,150,291,304,316,345],"repeated":[14],"measurements":[15],"collected":[16],"before,":[17],"during,":[18],"or":[19,88,115],"after":[20,198],"an":[21,59,96],"intervention.":[22],"Existing":[23],"approaches,":[24],"including":[25,119],"mixed-effects":[26,123],"models":[27],"and":[28,66,107,128,148,164,184,201,214,232,264,277,286,319,331,343],"generalized":[29,125],"additive":[30,126],"models,":[31,124,127],"estimate":[32],"temporal":[33,299,317,346],"effects":[34],"but":[35],"do":[36],"not":[37,266],"generally":[38],"provide":[39,139],"discrete":[41],"representation":[42,65,142,315],"trajectory":[44,105,155,293,336,349],"topology":[45,242,302],"that":[46,255],"can":[47,108],"be":[48,110],"queried":[49],"directly":[50,313],"across":[51],"experimental":[52],"groups.":[53],"1.2":[54],"Methods":[55],"We":[56,157],"developed":[57],"LongOmicsTraj,":[58],"open-source":[60],"R":[61],"package":[62],"for":[63,143,280],"topology-based":[64,144],"querying":[67],"short":[69,322],"trajectories.":[72],"The":[73,187,270],"framework":[74,160],"encodes":[75],"the":[76,92,159,170,236],"direction":[77,318],"change":[79],"between":[80],"adjacent":[81],"visits":[82],"as":[83,154],"up":[84],",":[85,87,90],"down":[86],"flat":[89],"with":[91,217,226,301],"ordered":[93],"sequence":[94],"defining":[95],"Ordinal":[97],"Trajectory":[98],"State":[99],"(OTS).":[100],"LongOmicsTraj":[101,207,309],"operates":[102],"downstream":[103],"estimation":[106,330],"therefore":[109],"applied":[111],"to":[112,248],"empirical":[113],"summaries":[114],"model-derived":[116],"visit-level":[117],"estimates,":[118],"those":[120],"from":[121,169],"linear":[122],"polynomial":[129],"regression,":[130],"following":[131,262],"maSigPro-style":[133],"time-course":[134],"formulation":[135],"[1].":[136],"OTS":[137],"labels":[138],"common":[141],"querying,":[145],"cross-group":[146,341],"comparison,":[147],"evaluation":[149,290],"higher-level":[151],"representations":[152],"such":[153],"clusters.":[156,350],"evaluated":[158],"using":[161],"controlled":[162],"simulations":[163],"bronchial":[165],"biopsy":[166],"transcriptomic":[167],"data":[168],"GLUCOLD":[171],"corticosteroid":[172,193,253],"intervention":[173],"study":[174],"(GEO":[175],"accession":[176],"GSE36221":[177],"),":[178],"measured":[179,246],"at":[180],"baseline,":[181],"6":[182,199],"months,":[183,200],"30":[185],"months.":[186],"biological":[188],"analysis":[189],"compared":[190],"continued":[191,259],"inhaled":[192],"(ICS)":[194],"treatment,":[195,260],"ICS":[196],"withdrawal":[197],"placebo.":[202,269],"1.3":[203],"Results":[204],"In":[205,239],"simulations,":[206],"recovered":[208],"predefined":[209],"stable,":[210],"monotonic,":[211],"transient,":[212],"rebound,":[213],"oscillatory":[215],"trajectories":[216],"high":[218],"accuracy":[219],"when":[220],"signal":[222],"was":[223,256,265],"sufficiently":[224],"clear,":[225],"performance":[227],"declining":[228],"under":[229,268],"high-noise":[230],"conditions":[231],"depending":[233],"partly":[234],"on":[235],"upstream":[237],"estimator.":[238],"GLUCOLD,":[240],"comparator-aware":[241],"queries":[243,342],"reduced":[244],"20,358":[245],"transcripts":[247],"168":[249],"genes":[250,272,276],"showing":[251],"response":[254],"maintained":[257],"during":[258],"reversed":[261],"withdrawal,":[263],"reproduced":[267],"selected":[271],"included":[273],"established":[274],"corticosteroid-response":[275],"were":[278],"enriched":[279],"immune-cell":[281],"migration,":[282],"chemotaxis,":[283],"cell":[284],"adhesion,":[285],"extracellular-matrix":[287],"organisation.":[288],"Topology-aware":[289],"FlexMix":[292],"clusters":[294],"additionally":[295],"revealed":[296],"substantial":[297],"within-cluster":[298],"heterogeneity,":[300],"purities":[303],"approximately":[305],"46\u201360%.":[306],"1.4":[307],"Conclusions":[308],"provides":[310],"compact,":[312],"queryable":[314],"order":[320],"in":[321],"studies.":[325],"It":[326],"complements":[327],"existing":[328],"clustering":[332],"methods":[333],"by":[334],"making":[335],"structure":[337],"explicit,":[338],"enabling":[339],"structured":[340],"quantification":[344],"heterogeneity":[347],"within":[348]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-08-23T00:00:00"}