{"id":"https://openalex.org/W4304128258","doi":"https://doi.org/10.3390/a15100371","title":"Topological Data Analysis in Time Series: Temporal Filtration and Application to Single-Cell Genomics","display_name":"Topological Data Analysis in Time Series: Temporal Filtration and Application to Single-Cell Genomics","publication_year":2022,"publication_date":"2022-10-10","ids":{"openalex":"https://openalex.org/W4304128258","doi":"https://doi.org/10.3390/a15100371"},"language":"en","primary_location":{"id":"doi:10.3390/a15100371","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a15100371","pdf_url":"https://www.mdpi.com/1999-4893/15/10/371/pdf?version=1666684001","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/15/10/371/pdf?version=1666684001","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018612055","display_name":"Baihan Lin","orcid":"https://orcid.org/0000-0002-7979-5509"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]},{"id":"https://openalex.org/I2799503643","display_name":"Columbia University Irving Medical Center","ror":"https://ror.org/01esghr10","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799503643"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Baihan Lin","raw_affiliation_strings":["Department of Neuroscience, Columbia University Irving Medical Center, New York, NY 10032, USA","Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA","Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, Columbia University Irving Medical Center, New York, NY 10032, USA","institution_ids":["https://openalex.org/I2799503643"]},{"raw_affiliation_string":"Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA","institution_ids":["https://openalex.org/I2799503643"]},{"raw_affiliation_string":"Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5018612055"],"corresponding_institution_ids":["https://openalex.org/I2799503643","https://openalex.org/I78577930"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":1.0224,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.79219799,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"15","issue":"10","first_page":"371","last_page":"371"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12536","display_name":"Topological and Geometric Data Analysis","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12536","display_name":"Topological and Geometric Data Analysis","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9932000041007996,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9688000082969666,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/series","display_name":"Series (stratigraphy)","score":0.6445688605308533},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6033785343170166},{"id":"https://openalex.org/keywords/filtration","display_name":"Filtration (mathematics)","score":0.5954874753952026},{"id":"https://openalex.org/keywords/topological-data-analysis","display_name":"Topological data analysis","score":0.5829063653945923},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5750276446342468},{"id":"https://openalex.org/keywords/time-series","display_name":"Time series","score":0.5451177954673767},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.44460269808769226},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4100833833217621},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.38546186685562134},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3104995787143707},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2524968683719635},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.25222790241241455},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23880615830421448},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.19123122096061707},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.15660050511360168},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.13708296418190002},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13195207715034485},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09606271982192993},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09319579601287842}],"concepts":[{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.6445688605308533},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6033785343170166},{"id":"https://openalex.org/C128489963","wikidata":"https://www.wikidata.org/wiki/Q1187724","display_name":"Filtration (mathematics)","level":2,"score":0.5954874753952026},{"id":"https://openalex.org/C2776477805","wikidata":"https://www.wikidata.org/wiki/Q4460773","display_name":"Topological data analysis","level":2,"score":0.5829063653945923},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5750276446342468},{"id":"https://openalex.org/C151406439","wikidata":"https://www.wikidata.org/wiki/Q186588","display_name":"Time series","level":2,"score":0.5451177954673767},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.44460269808769226},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4100833833217621},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.38546186685562134},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3104995787143707},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2524968683719635},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25222790241241455},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23880615830421448},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.19123122096061707},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.15660050511360168},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.13708296418190002},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13195207715034485},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09606271982192993},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09319579601287842},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/a15100371","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a15100371","pdf_url":"https://www.mdpi.com/1999-4893/15/10/371/pdf?version=1666684001","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:3d46ef5cf29447639f44418a25e6bd0b","is_oa":true,"landing_page_url":"https://doaj.org/article/3d46ef5cf29447639f44418a25e6bd0b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms, Vol 15, Iss 10, p 371 (2022)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1999-4893/15/10/371/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/a15100371","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms; Volume 15; Issue 10; Pages: 371","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/a15100371","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a15100371","pdf_url":"https://www.mdpi.com/1999-4893/15/10/371/pdf?version=1666684001","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6899999976158142,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4304128258.pdf","grobid_xml":"https://content.openalex.org/works/W4304128258.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W28435248","https://openalex.org/W85047175","https://openalex.org/W1486210143","https://openalex.org/W1607787316","https://openalex.org/W1829183947","https://openalex.org/W1970032869","https://openalex.org/W1991566301","https://openalex.org/W2020428772","https://openalex.org/W2071391326","https://openalex.org/W2087242711","https://openalex.org/W2102212449","https://openalex.org/W2115445832","https://openalex.org/W2148676644","https://openalex.org/W2162376722","https://openalex.org/W2187089797","https://openalex.org/W2223140295","https://openalex.org/W2610774430","https://openalex.org/W2759265966","https://openalex.org/W2765713566","https://openalex.org/W2788348358","https://openalex.org/W2797507693","https://openalex.org/W2800912249","https://openalex.org/W2889326414","https://openalex.org/W2892146033","https://openalex.org/W2964534207","https://openalex.org/W2967437913","https://openalex.org/W2980929630","https://openalex.org/W3002770500","https://openalex.org/W3007158032","https://openalex.org/W3014671498","https://openalex.org/W3098455240","https://openalex.org/W3099810371","https://openalex.org/W3104997105","https://openalex.org/W4220911478","https://openalex.org/W4389192063","https://openalex.org/W6603472029"],"related_works":["https://openalex.org/W4390608645","https://openalex.org/W4247566972","https://openalex.org/W4394895745","https://openalex.org/W2960264696","https://openalex.org/W3090563135","https://openalex.org/W2497432351","https://openalex.org/W4206777497","https://openalex.org/W2910064364","https://openalex.org/W4200136508","https://openalex.org/W4394629176"],"abstract_inverted_index":{"The":[0],"absence":[1],"of":[2,22,38,58,63,101,115,123,125,135,149,163],"a":[3,48,111,193],"conventional":[4],"association":[5],"between":[6],"the":[7,31,35,56,59,64,74,79,93,133,154,159,181,187],"cell\u2013cell":[8],"cohabitation":[9],"and":[10,28,68,172,196],"its":[11],"emergent":[12],"dynamics":[13],"into":[14,129],"cliques":[15,124],"during":[16],"development":[17],"has":[18],"hindered":[19],"our":[20,176,199],"understanding":[21],"how":[23],"cell":[24,32,170,208],"populations":[25],"proliferate,":[26],"differentiate,":[27],"compete":[29],"(i.e.,":[30],"ecology).":[33],"With":[34],"recent":[36],"advancement":[37],"single-cell":[39,84,94,126,160],"RNA":[40],"sequencing":[41],"(RNA-seq),":[42],"we":[43],"can":[44,201],"potentially":[45],"describe":[46],"such":[47],"link":[49],"by":[50,78],"constructing":[51],"network":[52],"graphs":[53,71],"that":[54,131],"characterize":[55],"similarity":[57],"gene":[60,95],"expression":[61,96],"profiles":[62,97,127],"cell-specific":[65],"transcriptional":[66],"programs":[67],"analyze":[69],"these":[70,142,150],"systematically":[72],"using":[73],"summary":[75],"statistics":[76],"given":[77],"algebraic":[80],"topology.":[81],"We":[82,140],"propose":[83],"topological":[85,146],"simplicial":[86,147],"analysis":[87],"(scTSA).":[88],"Applying":[89],"this":[90],"approach":[91,177,200],"to":[92,205],"from":[98],"local":[99],"networks":[100,119],"cells":[102],"in":[103,189],"different":[104,108],"developmental":[105,190],"stages":[106],"with":[107,145,153,186],"outcomes":[109],"reveals":[110],"previously":[112],"unseen":[113],"topology":[114],"cellular":[116],"ecology.":[117],"These":[118],"contain":[120],"an":[121],"abundance":[122],"bound":[128],"cavities":[130],"guide":[132],"emergence":[134],"more":[136],"complicated":[137],"habitation":[138],"forms.":[139],"visualize":[141],"ecological":[143],"patterns":[144],"architectures":[148],"networks,":[151],"compared":[152],"null":[155],"models.":[156],"Benchmarked":[157],"on":[158],"RNA-seq":[161],"data":[162],"zebrafish":[164],"embryogenesis":[165],"spanning":[166],"38,731":[167],"cells,":[168],"25":[169],"types,":[171],"12":[173],"time":[174],"steps,":[175],"highlights":[178],"gastrulation":[179],"as":[180],"most":[182],"critical":[183,211],"stage,":[184],"consistent":[185],"consensus":[188],"biology.":[191],"As":[192],"nonlinear,":[194],"model-independent,":[195],"unsupervised":[197],"framework,":[198],"also":[202],"be":[203],"applied":[204],"tracing":[206],"multi-scale":[207],"lineage,":[209],"identifying":[210],"stages,":[212],"or":[213],"creating":[214],"pseudo-time":[215],"series.":[216]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}