{"id":"https://openalex.org/W7203967306","doi":"https://doi.org/10.64898/2026.08.20.746066","title":"A reusable neural approach to recombination mapping for model and non-model species","display_name":"A reusable neural approach to recombination mapping for model and non-model species","publication_year":2026,"publication_date":"2026-08-22","ids":{"openalex":"https://openalex.org/W7203967306","doi":"https://doi.org/10.64898/2026.08.20.746066","pmid":"https://pubmed.ncbi.nlm.nih.gov/42922456","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13684450"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.20.746066","doi":"https://doi.org/10.64898/2026.08.20.746066","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.20.746066","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/22/2026.08.20.746066.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/22/2026.08.20.746066.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051766459","display_name":"Kevin Korfmann","orcid":"https://orcid.org/0000-0001-8869-8949","observed_orcids":["https://orcid.org/0000-0001-8869-8949"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kevin Korfmann","raw_affiliation_strings":["Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"],"raw_orcid":"https://orcid.org/0000-0001-8869-8949","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115691644","display_name":"Neda Rahnamae","orcid":"https://orcid.org/0009-0005-1607-0323","observed_orcids":["https://orcid.org/0009-0005-1607-0323"]},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Neda Rahnamae","raw_affiliation_strings":["Institute of Plant Ecology and Evolution, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"],"raw_orcid":"https://orcid.org/0009-0005-1607-0323","affiliations":[{"raw_affiliation_string":"Institute of Plant Ecology and Evolution, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002178567","display_name":"Sara Mathieson","orcid":"https://orcid.org/0000-0002-0484-0838","observed_orcids":["https://orcid.org/0000-0002-0484-0838"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sara Mathieson","raw_affiliation_strings":["Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"],"raw_orcid":"https://orcid.org/0000-0002-0484-0838","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5051766459"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.6880000233650208,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.6880000233650208,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10012","display_name":"Genetic diversity and population structure","score":0.17479999363422394,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.032999999821186066,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/recombination-mapping","display_name":"recombination mapping","score":0.9789999723434448},{"id":"https://openalex.org/keywords/linkage-disequilibrium","display_name":"linkage disequilibrium","score":0.9020000100135803},{"id":"https://openalex.org/keywords/recombination-rate-variation","display_name":"recombination rate variation","score":0.7310000061988831},{"id":"https://openalex.org/keywords/state-space-neural-networks","display_name":"state-space neural networks","score":0.8579999804496765},{"id":"https://openalex.org/keywords/arabis","display_name":"Arabis","score":0.7789999842643738},{"id":"https://openalex.org/keywords/malaria-vectors","display_name":"malaria vectors","score":0.7459999918937683},{"id":"https://openalex.org/keywords/anopheles-gambiae","display_name":"Anopheles gambiae","score":0.8009999990463257},{"id":"https://openalex.org/keywords/supergenes","display_name":"supergenes","score":0.5630000233650208},{"id":"https://openalex.org/keywords/structural-variants","display_name":"structural variants","score":0.6679999828338623},{"id":"https://openalex.org/keywords/selection","display_name":"selection","score":0.5649999976158142},{"id":"https://openalex.org/keywords/resistance-loci","display_name":"resistance loci","score":0.6029999852180481}],"concepts":[{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.4864000082015991},{"id":"https://openalex.org/C35605836","wikidata":"https://www.wikidata.org/wiki/Q2064311","display_name":"Linkage disequilibrium","level":5,"score":0.4823000133037567},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4523000121116638},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.43970000743865967},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4307999908924103},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4092999994754791},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.4090000092983246},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39340001344680786},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.38850000500679016},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.3849000036716461},{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.3646000027656555},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.3522999882698059},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.3402000069618225},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.32739999890327454},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.31520000100135803},{"id":"https://openalex.org/C85721925","wikidata":"https://www.wikidata.org/wiki/Q31151","display_name":"Population genetics","level":3,"score":0.2969000041484833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.290800005197525},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2854999899864197},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.2806999981403351},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.2773999869823456},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.26899999380111694},{"id":"https://openalex.org/C22593422","wikidata":"https://www.wikidata.org/wiki/Q3242583","display_name":"Pedigree chart","level":3,"score":0.266400009393692},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.26080000400543213},{"id":"https://openalex.org/C49735019","wikidata":"https://www.wikidata.org/wiki/Q4115005","display_name":"Selective sweep","level":5,"score":0.2540999948978424}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.64898/2026.08.20.746066","doi":"https://doi.org/10.64898/2026.08.20.746066","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.20.746066","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/22/2026.08.20.746066.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:13684450","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13684450/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13684450/pdf/nihpp-2026.08.20.746066v2.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"},{"id":"pmid:42922456","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42922456","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.64898/2026.08.20.746066","doi":"https://doi.org/10.64898/2026.08.20.746066","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.20.746066","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/22/2026.08.20.746066.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G6462795265","display_name":null,"funder_award_id":"https://ror.org/01cwqze88 (Grant: R15HG011528)","funder_id":"https://openalex.org/F4320338403","funder_display_name":"Common Fund"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338403","display_name":"Common Fund","ror":"https://ror.org/001d55x84"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7203967306.pdf","grobid_xml":"https://content.openalex.org/works/W7203967306.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1911481782","https://openalex.org/W1964558095","https://openalex.org/W1972266804","https://openalex.org/W1978025281","https://openalex.org/W1984471144","https://openalex.org/W2005739865","https://openalex.org/W2030191595","https://openalex.org/W2051598862","https://openalex.org/W2060811895","https://openalex.org/W2084597370","https://openalex.org/W2085231911","https://openalex.org/W2085502859","https://openalex.org/W2111534865","https://openalex.org/W2119279196","https://openalex.org/W2130315111","https://openalex.org/W2136832363","https://openalex.org/W2142417092","https://openalex.org/W2147039800","https://openalex.org/W2153432101","https://openalex.org/W2154160289","https://openalex.org/W2166238348","https://openalex.org/W2170301165","https://openalex.org/W2314051380","https://openalex.org/W2419574648","https://openalex.org/W2516145265","https://openalex.org/W2564456678","https://openalex.org/W2719263793","https://openalex.org/W2793222991","https://openalex.org/W2915041973","https://openalex.org/W2949516520","https://openalex.org/W2973699867","https://openalex.org/W2973916336","https://openalex.org/W2981354404","https://openalex.org/W2987904511","https://openalex.org/W3008479721","https://openalex.org/W3092862378","https://openalex.org/W3128087295","https://openalex.org/W4207021253","https://openalex.org/W4220997876","https://openalex.org/W4221069327","https://openalex.org/W4392918118","https://openalex.org/W4396946579","https://openalex.org/W4416729254","https://openalex.org/W4417221216","https://openalex.org/W7169826485"],"related_works":["https://openalex.org/W2948989750","https://openalex.org/W3008479721","https://openalex.org/W4405805824","https://openalex.org/W4291224151","https://openalex.org/W2126491299","https://openalex.org/W4315489214","https://openalex.org/W4353079163","https://openalex.org/W1199732744","https://openalex.org/W4381715352","https://openalex.org/W7095142170"],"abstract_inverted_index":{"Abstract":[0],"Pedigree":[1],"and":[2,9,61,83,138,192,199],"crossing":[3],"experiments":[4],"can":[5],"measure":[6],"crossovers":[7],"directly":[8],"provide":[10,34],"the":[11,45,86,104,123,149,153,172],"gold":[12],"standard":[13],"for":[14,39,117,130,184,211,223],"recombination":[15,22,43,158,225],"mapping,":[16],"but":[17],"their":[18],"cost":[19],"restricts":[20],"fine-scale":[21],"mapping":[23,226],"to":[24,115],"only":[25],"a":[26,69,75,156,165,220],"few":[27],"species.":[28],"Patterns":[29],"of":[30,77,148,155,168,189],"linkage":[31],"disequilibrium":[32],"(LD)":[33],"an":[35],"alternative":[36],"statistical":[37],"approach":[38],"inferring":[40],"variation":[41,170,201],"in":[42,122,132],"along":[44],"genome.":[46],"LD,":[47],"however,":[48],"is":[49],"confounded":[50],"by":[51],"many":[52],"evolutionary":[53],"factors,":[54],"such":[55],"as":[56,219],"demographic":[57],"changes,":[58],"life-history":[59],"traits,":[60],"genomic":[62],"structural":[63,200],"variation.":[64],"We":[65,107],"present":[66],"fastrho":[67,218],",":[68],"state-space":[70],"neural-network":[71],"estimator":[72],"trained":[73],"across":[74,111,171,227],"range":[76],"simulation-based":[78],"priors.":[79],"In":[80],"simulated":[81],"bottleneck":[82],"expansion":[84],"scenarios,":[85],"fixed":[87],"checkpoint":[88],"recovered":[89],"local":[90],"map":[91],"shape":[92],"without":[93],"target-specific":[94],"retraining;":[95],"comparisons":[96],"with":[97],"pyrho":[98],"used":[99],"lookup":[100],"tables":[101],"constructed":[102],"under":[103],"simulation-generating":[105],"history.":[106],"further":[108],"evaluated":[109],"generalizability":[110],"multiple":[112],"species":[113],"and,":[114],"account":[116],"additional":[118],"confounders":[119],"not":[120],"represented":[121],"initial":[124],"training":[125],"data,":[126],"designed":[127],"specialized":[128],"models":[129],"inference":[131],"selfing":[133],"plants,":[134],"structured":[135],"Arabis":[136],"populations,":[137,163],"large-":[139],"N":[140],"e":[141],"malaria-vector":[142],"populations.":[143],"A":[144],"major":[145],"biological":[146,229],"application":[147],"mosquito":[150],"model":[151],"was":[152],"construction":[154],"five-arm":[157],"atlas":[159],"spanning":[160],"13":[161],"Ag3":[162,178],"providing":[164],"detailed":[166],"view":[167],"recombination-rate":[169],"dataset.":[173],"Recombination":[174],"maps":[175,210],"inferred":[176],"from":[177],"pedigrees":[179],"provided":[180],"independent,":[181],"coarse-scale":[182],"support":[183],"this":[185],"atlas.":[186],"Finally,":[187],"analyses":[188],"resistance":[190],"loci":[191],"redpoll":[193],"bird":[194],"supergenes":[195],"demonstrate":[196],"how":[197],"selection":[198],"influence":[202],"LD.":[203],"Throughout":[204],"our":[205,215],"study,":[206],"we":[207],"use":[208],"experimental":[209],"independent":[212],"validation.":[213],"Together,":[214],"results":[216],"establish":[217],"flexible":[221],"framework":[222],"robust":[224],"diverse":[228],"systems.":[230]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-08-23T00:00:00"}
