{"id":"https://openalex.org/W7225809290","doi":"https://doi.org/10.64898/2026.11.10.765665","title":"Inferring chromatin looping interactions from microscopy-based measurements: opportunities and pitfalls","display_name":"Inferring chromatin looping interactions from microscopy-based measurements: opportunities and pitfalls","publication_year":2026,"publication_date":"2026-11-11","ids":{"openalex":"https://openalex.org/W7225809290","doi":"https://doi.org/10.64898/2026.11.10.765665"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.10.765665","doi":"https://doi.org/10.64898/2026.11.10.765665","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.10.765665","pdf_url":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.11.10.765665","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037478498","display_name":"James M. Jusuf","orcid":"https://orcid.org/0000-0002-2786-5982","observed_orcids":["https://orcid.org/0000-0002-2786-5982"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James M Jusuf","raw_affiliation_strings":["MIT;"],"raw_orcid":"https://orcid.org/0000-0002-2786-5982","affiliations":[{"raw_affiliation_string":"MIT;","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049740611","display_name":"Anders S. Hansen","orcid":"https://orcid.org/0000-0001-7540-7858","observed_orcids":["https://orcid.org/0000-0001-7540-7858"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anders Sejr Hansen","raw_affiliation_strings":["MIT;"],"raw_orcid":"https://orcid.org/0000-0001-7540-7858","affiliations":[{"raw_affiliation_string":"MIT;","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084982232","display_name":"Christoph Zechner","orcid":"https://orcid.org/0000-0003-1300-6076","observed_orcids":["https://orcid.org/0000-0003-1300-6076"]},"institutions":[{"id":"https://openalex.org/I138549579","display_name":"Scuola Internazionale Superiore di Studi Avanzati","ror":"https://ror.org/004fze387","country_code":"IT","type":"education","lineage":["https://openalex.org/I138549579"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Christoph Zechner","raw_affiliation_strings":["SISSA"],"raw_orcid":"https://orcid.org/0000-0003-1300-6076","affiliations":[{"raw_affiliation_string":"SISSA","institution_ids":["https://openalex.org/I138549579"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8320000171661377,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8320000171661377,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.07150000333786011,"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"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.01979999989271164,"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":[],"concepts":[{"id":"https://openalex.org/C191178318","wikidata":"https://www.wikidata.org/wiki/Q2256906","display_name":"Thresholding","level":3,"score":0.7081000208854675},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6051999926567078},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5723000168800354},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.5669000148773193},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4390000104904175},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.420199990272522},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4088999927043915},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3774999976158142},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3391000032424927},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.33390000462532043},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3292999863624573},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.29420000314712524},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2867000102996826},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.27140000462532043},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.2572000026702881},{"id":"https://openalex.org/C2777317252","wikidata":"https://www.wikidata.org/wiki/Q18393516","display_name":"Rare events","level":2,"score":0.25429999828338623}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.10.765665","doi":"https://doi.org/10.64898/2026.11.10.765665","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.10.765665","pdf_url":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.10.765665","doi":"https://doi.org/10.64898/2026.11.10.765665","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.10.765665","pdf_url":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Chromatin":[0],"looping":[1,29,40,79,124],"plays":[2],"essential":[3],"roles":[4],"in":[5,23,75,128],"several":[6],"nuclear":[7],"processes":[8],"and":[9,32,82],"live-cell":[10],"microscopy":[11],"has":[12],"become":[13],"a":[14],"key":[15],"method":[16,65],"for":[17],"studying":[18],"how":[19,116],"chromatin":[20],"loops":[21],"behave":[22],"time.":[24,84],"Extracting":[25],"dynamical":[26],"parameters":[27,125],"including":[28],"probability,":[30,80],"lifetime,":[31,81],"search":[33,83],"time":[34],"from":[35,42,94],"live-imaging":[36],"data":[37,51],"requires":[38],"inferring":[39],"events":[41],"noisy":[43],"3D":[44,70],"distance":[45,71],"trajectories.":[46],"By":[47],"analyzing":[48],"polymer":[49],"simulation":[50],"with":[52,59],"known":[53],"ground":[54],"truth,":[55],"we":[56,114],"show":[57,91],"that":[58,92],"realistic":[60],"localization":[61,100],"precision,":[62],"the":[63,105,108],"common":[64],"of":[66,78,107],"simple":[67,87,95],"thresholding":[68,96],"on":[69],"measurements":[72],"can":[73,119],"result":[74],"severe":[76],"misestimation":[77],"We":[85],"use":[86],"statistical":[88],"considerations":[89],"to":[90,104,110,122],"inference":[93],"becomes":[97],"infeasible":[98],"when":[99],"error":[101],"is":[102],"comparable":[103],"size":[106],"interaction":[109],"be":[111,120],"studied.":[112],"Finally,":[113],"demonstrate":[115],"noise-aware":[117],"methods":[118],"used":[121],"estimate":[123],"more":[126],"accurately":[127],"these":[129],"regimes.":[130]},"counts_by_year":[],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2026-11-12T00:00:00"}