{"id":"https://openalex.org/W4409727666","doi":"https://doi.org/10.1101/2025.04.16.649183","title":"ChromeCRISPR - A High Efficacy Hybrid Machine Learning Model for CRISPR/Cas On-Target Predictions","display_name":"ChromeCRISPR - A High Efficacy Hybrid Machine Learning Model for CRISPR/Cas On-Target Predictions","publication_year":2025,"publication_date":"2025-04-16","ids":{"openalex":"https://openalex.org/W4409727666","doi":"https://doi.org/10.1101/2025.04.16.649183"},"language":"en","primary_location":{"id":"doi:10.1101/2025.04.16.649183","doi":"https://doi.org/10.1101/2025.04.16.649183","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.16.649183","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/04/16/2025.04.16.649183.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/2025/04/16/2025.04.16.649183.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092098593","display_name":"Amirhossein Daneshpajouh","orcid":"https://orcid.org/0000-0002-1596-3446","observed_orcids":["https://orcid.org/0000-0002-1596-3446"]},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Amirhossein Daneshpajouh","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, 8888 University Dr W, Burnaby, Canada"],"raw_orcid":"https://orcid.org/0000-0002-1596-3446","affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, 8888 University Dr W, Burnaby, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104081400","display_name":"Megan Fowler","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Megan Fowler","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, 8888 University Dr W, Burnaby, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, 8888 University Dr W, Burnaby, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049270004","display_name":"Kay C. Wiese","orcid":"https://orcid.org/0000-0003-4507-1892","observed_orcids":["https://orcid.org/0000-0003-4507-1892"]},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Kay C. Wiese","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, 8888 University Dr W, Burnaby, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, 8888 University Dr W, Burnaby, Canada","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5049270004"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9994999766349792,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9994999766349792,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":9.999999747378752e-05,"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/T12610","display_name":"RNA regulation and disease","score":0.0,"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/crispr-cas9","display_name":"CRISPR/Cas9","score":0.9729999899864197},{"id":"https://openalex.org/keywords/single-guide-rna","display_name":"single guide RNA","score":0.7760000228881836},{"id":"https://openalex.org/keywords/genome-editing","display_name":"genome editing","score":0.8199999928474426},{"id":"https://openalex.org/keywords/hybrid-cnn-rnn-model","display_name":"hybrid CNN-RNN model","score":0.8820000290870667},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC content","score":0.9670000076293945},{"id":"https://openalex.org/keywords/benchmark-dataset","display_name":"benchmark dataset","score":0.3440000116825104}],"concepts":[{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.8979009389877319},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.621961236000061},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46657881140708923},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3518293797969818},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33444806933403015},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20332416892051697},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06874710321426392},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2025.04.16.649183","doi":"https://doi.org/10.1101/2025.04.16.649183","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.16.649183","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/04/16/2025.04.16.649183.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:10.1101/2025.04.16.649183","doi":"https://doi.org/10.1101/2025.04.16.649183","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.04.16.649183","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/04/16/2025.04.16.649183.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":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G7542484178","display_name":null,"funder_award_id":"RGPIN/04971-2020","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320331257","display_name":"Alliance de recherche num\u00e9rique du Canada","ror":"https://ror.org/010r6td27"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409727666.pdf","grobid_xml":"https://content.openalex.org/works/W4409727666.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1594078235","https://openalex.org/W1832693441","https://openalex.org/W1869792624","https://openalex.org/W1915704240","https://openalex.org/W1968342623","https://openalex.org/W1981276685","https://openalex.org/W2012034410","https://openalex.org/W2031211461","https://openalex.org/W2036176224","https://openalex.org/W2045435533","https://openalex.org/W2047032063","https://openalex.org/W2101234009","https://openalex.org/W2133564696","https://openalex.org/W2154598603","https://openalex.org/W2163241233","https://openalex.org/W2188223075","https://openalex.org/W2224398381","https://openalex.org/W2252568502","https://openalex.org/W2259938310","https://openalex.org/W2318802957","https://openalex.org/W2554763217","https://openalex.org/W2584973635","https://openalex.org/W2765284830","https://openalex.org/W2919831875","https://openalex.org/W2938071844","https://openalex.org/W2970971581","https://openalex.org/W2973312556","https://openalex.org/W2982510384","https://openalex.org/W2991600264","https://openalex.org/W2993948503","https://openalex.org/W2998932094","https://openalex.org/W3003257820","https://openalex.org/W3005962315","https://openalex.org/W3016213906","https://openalex.org/W3026538346","https://openalex.org/W3088092039","https://openalex.org/W3133793116","https://openalex.org/W3134782704","https://openalex.org/W3135625811","https://openalex.org/W3174495281","https://openalex.org/W4221016141","https://openalex.org/W4366551165","https://openalex.org/W4379521490","https://openalex.org/W4387251159"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4213036952","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4377030018","https://openalex.org/W4364306694"],"abstract_inverted_index":{"Abstract":[0],"Genome":[1],"editing":[2,35],"has":[3,216],"the":[4,11,19,23,49,61,71,83,100,105,108,121,145,152,157,171,203],"potential":[5],"to":[6,59,64,70,81,110,112,149,167,180],"treat":[7],"genetic":[8],"disorders":[9],"at":[10,73],"source.":[12],"This":[13,135],"can":[14,140],"be":[15],"achieved":[16],"by":[17,143],"modifying":[18],"defective":[20],"DNA":[21,67,89,115],"through":[22],"intentional":[24],"insertion,":[25],"deletion,":[26],"or":[27],"substitution":[28],"of":[29,99,107,147,155,173,205],"genomic":[30],"content.":[31],"Among":[32],"all":[33],"genome":[34],"technologies,":[36],"CRISPR/Cas":[37,52,84,183],"(Clustered":[38],"Regularly":[39],"Interspaced":[40],"Short":[41],"Palindromic":[42],"Repeats":[43],"and":[44,169,222],"CRISPR-associated":[45],"protein)":[46],"is":[47,79,102,127,136],"considered":[48],"gold":[50],"standard.":[51],"uses":[53],"a":[54,65,94,113,124,163,225],"single":[55],"guide":[56],"RNA":[57,76],"(sgRNA)":[58],"direct":[60],"Cas":[62],"nuclease":[63],"target":[66,86],"region.":[68],"Due":[69],"ease":[72],"creating":[74],"small":[75],"molecules,":[77],"it":[78,93],"possible":[80],"have":[82,132,161],"complex":[85,101],"any":[87],"arbitrary":[88],"sequence,":[90,116],"thus":[91],"making":[92],"versatile":[95],"tool.":[96],"The":[97],"efficacy":[98,233],"dependent":[103],"on":[104,120],"ability":[106,172,179],"sgRNA":[109,129,194],"bind":[111],"complementary":[114],"which":[117],"varies":[118],"based":[119],"sequence.":[122],"Thus,":[123],"major":[125],"challenge":[126],"finding":[128,156],"sequences":[130],"that":[131],"good":[133],"efficacy.":[134],"where":[137],"computational":[138],"models":[139],"aid":[141],"scientists:":[142],"predicting":[144],"activity":[146,195],"sgRNAs":[148],"help":[150],"narrow":[151],"search":[153],"space":[154],"optimal":[158],"sgRNA.":[159],"We":[160],"used":[162],"large":[164],"new":[165,226],"dataset":[166],"build":[168],"compare":[170],"several":[174],"different":[175],"machine":[176],"learning":[177],"architectures\u2019":[178],"predict":[181],"on-target":[182],"activity.":[184],"Additionally,":[185],"we":[186],"explored":[187],"how":[188],"adding":[189],"GC":[190],"content":[191],"affects":[192],"our":[193],"predictions.":[196,234],"Our":[197],"novel":[198],"hybrid":[199],"model,":[200],"ChromeCRISPR,":[201],"combines":[202],"strengths":[204],"Convolutional":[206],"Neural":[207,212],"Networks":[208],"(CNN)":[209],"with":[210],"Recurrent":[211],"Network":[213],"(RNN)":[214],"models,":[215,219],"outperformed":[217],"state-of-the-art":[218],"including":[220],"DeepHF":[221],"AttCrispr,":[223],"establishing":[224],"benchmark":[227],"for":[228],"predictive":[229],"accuracy":[230],"in":[231],"CRISPR/Cas9":[232]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2025-10-10T00:00:00"}