{"id":"https://openalex.org/W7205006893","doi":"https://doi.org/10.64898/2026.08.31.748412","title":"BARCS: beta-binomial regression for multivariable CRISPR screen designs","display_name":"BARCS: beta-binomial regression for multivariable CRISPR screen designs","publication_year":2026,"publication_date":"2026-09-01","ids":{"openalex":"https://openalex.org/W7205006893","doi":"https://doi.org/10.64898/2026.08.31.748412"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.31.748412","doi":"https://doi.org/10.64898/2026.08.31.748412","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748412","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.31.748412.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":"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://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.31.748412.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5149073992","display_name":"Kyu-Won Lee","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyu-Won Lee","raw_affiliation_strings":["Baylor College of Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baylor College of Medicine","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006380454","display_name":"Hyun-Hwan Jeong","orcid":"https://orcid.org/0000-0001-5090-2422","observed_orcids":["https://orcid.org/0000-0001-5090-2422"]},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hyun-Hwan Jeong","raw_affiliation_strings":["Baylor College of Medicine"],"raw_orcid":"https://orcid.org/0000-0001-5090-2422","affiliations":[{"raw_affiliation_string":"Baylor College of Medicine","institution_ids":["https://openalex.org/I181547552"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5006380454"],"corresponding_institution_ids":["https://openalex.org/I181547552"],"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9911999702453613,"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":0.9911999702453613,"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":0.00039999998989515007,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.00039999998989515007,"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/beta-binomial-regression","display_name":"beta-binomial regression","score":0.7990000247955322},{"id":"https://openalex.org/keywords/crispr-screening","display_name":"CRISPR screen","score":0.7950000166893005},{"id":"https://openalex.org/keywords/bhabha-atomic-research-centre","display_name":"BARC","score":0.7160000205039978},{"id":"https://openalex.org/keywords/deseq2","display_name":"DESeq2","score":0.9520000219345093}],"concepts":[{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.5835999846458435},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.522599995136261},{"id":"https://openalex.org/C161584116","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate statistics","level":2,"score":0.5098999738693237},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.5060999989509583},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.47679999470710754},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.44510000944137573},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4375},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.43540000915527344},{"id":"https://openalex.org/C48921125","wikidata":"https://www.wikidata.org/wiki/Q10861030","display_name":"Linear regression","level":2,"score":0.4172999858856201},{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.40869998931884766},{"id":"https://openalex.org/C41426520","wikidata":"https://www.wikidata.org/wiki/Q1192065","display_name":"Point estimation","level":2,"score":0.3978999853134155},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.391400009393692},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.3894999921321869},{"id":"https://openalex.org/C152877465","wikidata":"https://www.wikidata.org/wiki/Q208042","display_name":"Regression analysis","level":2,"score":0.388700008392334},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.37689998745918274},{"id":"https://openalex.org/C177562468","wikidata":"https://www.wikidata.org/wiki/Q182893","display_name":"Dispersion (optics)","level":2,"score":0.3472999930381775},{"id":"https://openalex.org/C196083921","wikidata":"https://www.wikidata.org/wiki/Q7915758","display_name":"Variance (accounting)","level":2,"score":0.3188999891281128},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.3001999855041504},{"id":"https://openalex.org/C91998498","wikidata":"https://www.wikidata.org/wiki/Q1541178","display_name":"Contingency table","level":2,"score":0.29899999499320984},{"id":"https://openalex.org/C40696583","wikidata":"https://www.wikidata.org/wiki/Q989120","display_name":"Type I and type II errors","level":2,"score":0.29490000009536743},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.29440000653266907},{"id":"https://openalex.org/C203763787","wikidata":"https://www.wikidata.org/wiki/Q371029","display_name":"Null (SQL)","level":2,"score":0.2818000018596649},{"id":"https://openalex.org/C163175372","wikidata":"https://www.wikidata.org/wiki/Q3339222","display_name":"Linear model","level":2,"score":0.2800000011920929},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.27309998869895935},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2685000002384186},{"id":"https://openalex.org/C183763347","wikidata":"https://www.wikidata.org/wiki/Q120976","display_name":"Factorial","level":2,"score":0.2676999866962433},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.2662999927997589},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26420000195503235},{"id":"https://openalex.org/C34559072","wikidata":"https://www.wikidata.org/wiki/Q2334061","display_name":"Design of experiments","level":2,"score":0.2614000141620636},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2581000030040741},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2565999925136566},{"id":"https://openalex.org/C191988596","wikidata":"https://www.wikidata.org/wiki/Q628374","display_name":"Null hypothesis","level":2,"score":0.25440001487731934},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.2522999942302704},{"id":"https://openalex.org/C169222746","wikidata":"https://www.wikidata.org/wiki/Q4116558","display_name":"Factorial experiment","level":2,"score":0.25200000405311584}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.31.748412","doi":"https://doi.org/10.64898/2026.08.31.748412","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748412","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.31.748412.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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.31.748412","doi":"https://doi.org/10.64898/2026.08.31.748412","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.31.748412","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/01/2026.08.31.748412.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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309543","display_name":"Texas Children's Hospital","ror":"https://ror.org/05cz92x43"},{"id":"https://openalex.org/F4320317232","display_name":"Huffington Foundation","ror":"https://ror.org/04bcjs591"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7205006893.pdf","grobid_xml":"https://content.openalex.org/works/W7205006893.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W53657057","https://openalex.org/W90334641","https://openalex.org/W1497616403","https://openalex.org/W2036897871","https://openalex.org/W2070050178","https://openalex.org/W2081098333","https://openalex.org/W2100122648","https://openalex.org/W2106201557","https://openalex.org/W2110065044","https://openalex.org/W2121211805","https://openalex.org/W2124985265","https://openalex.org/W2137526110","https://openalex.org/W2146511318","https://openalex.org/W2152239989","https://openalex.org/W2154065358","https://openalex.org/W2179438025","https://openalex.org/W2190856209","https://openalex.org/W2201689894","https://openalex.org/W2466314544","https://openalex.org/W2533641274","https://openalex.org/W2727479110","https://openalex.org/W2735132087","https://openalex.org/W2904226822","https://openalex.org/W2911986456","https://openalex.org/W2913649454","https://openalex.org/W2950723166","https://openalex.org/W2951038219","https://openalex.org/W2969815104","https://openalex.org/W2972647388","https://openalex.org/W3005084688","https://openalex.org/W3029194094","https://openalex.org/W3119382661","https://openalex.org/W4200497629","https://openalex.org/W4285015066","https://openalex.org/W4399824445","https://openalex.org/W4409847048","https://openalex.org/W7161399076","https://openalex.org/W7161482456"],"related_works":["https://openalex.org/W2972647388","https://openalex.org/W4282959699","https://openalex.org/W4319058516","https://openalex.org/W4399824445","https://openalex.org/W3011425199","https://openalex.org/W6892997457","https://openalex.org/W3087510731","https://openalex.org/W3177922178","https://openalex.org/W4409847048","https://openalex.org/W3011118130"],"abstract_inverted_index":{"Abstract":[0],"Pooled":[1],"CRISPR":[2],"screens":[3],"increasingly":[4],"use":[5],"longitudinal,":[6],"donor-adjusted,":[7],"and":[8,42,70,111,124,133,232],"factorial":[9],"designs,":[10],"but":[11,127,152,187],"beta-binomial":[12,26,165,208,268],"screen":[13],"methods":[14],"have":[15],"largely":[16],"remained":[17,197],"limited":[18],"to":[19,28,65,141,266],"pairwise":[20],"comparisons.":[21],"BARCS":[22,96,199],"extends":[23],"the":[24,51,60,80,106,170,191,206,242,267],"library-total-conditional":[25,207],"model":[27,209],"guide-level":[29,116,221],"regression":[30],"with":[31,101,211],"an":[32,91,212],"arbitrary":[33],"design":[34],"matrix,":[35],"enabling":[36],"direct":[37],"estimation":[38],"of":[39,205,215],"time,":[40],"covariate,":[41],"interaction":[43],"effects.":[44],"In":[45,90],"four":[46,81],"replicate-complete":[47],"Cas13":[48],"screens,":[49],"adding":[50],"intermediate":[52],"time":[53],"point":[54],"modestly":[55],"improved":[56],"essential-gene":[57],"recovery.":[58],"Applying":[59],"same":[61],"non-targeting-control":[62],"scaling":[63,150],"rule":[64],"BARCS,":[66],"MAGeCK-MLE,":[67],"edgeR-QL,":[68],"DESeq2,":[69],"limma\u2013voom":[71],"produced":[72],"similar":[73],"calibration":[74,193,196],"across":[75],"all":[76],"five":[77],"methods,":[78],"while":[79],"alternatives":[82],"ranked":[83],"essential":[84],"genes":[85],"more":[86,98],"strongly":[87],"than":[88,105,145,248],"BARCS.":[89],"ordered-bin":[92],"IL2RA":[93],"screen,":[94],"donor-adjusted":[95],"recovered":[97],"validated":[99],"regulators":[100],"fewer":[102],"total":[103],"calls":[104],"matched":[107],"four-bin":[108],"MAGeCK-MLE":[109],"fit,":[110],"cross-fitted":[112],"controls":[113],"exposed":[114,130],"excess":[115],"significance.":[117],"Simulations":[118],"showed":[119,168],"gains":[120],"from":[121],"dispersion":[122,146],"moderation":[123],"control-based":[125],"denominators,":[126],"seed-specific":[128],"results":[129],"denominator":[131],"sensitivity":[132],"a":[134,202],"null":[135],"grid":[136],"localized":[137],"substantial":[138],"gene-level":[139,230],"error":[140],"correlated-guide":[142],"aggregation":[143,237],"rather":[144,247],"alone.":[147],"Aggregation-matched":[148],"control":[149],"reduced":[151],"did":[153,188],"not":[154,189,261],"eliminate":[155],"this":[156,252],"error.":[157],"An":[158],"external":[159],"audit":[160],"prompted":[161],"by":[162,225],"concerns":[163],"about":[164],"false":[166],"discoveries":[167],"that":[169,241],"reported":[171],"CB":[172],"2":[173],"null-discovery":[174],"count":[175],"disappeared":[176],"when":[177],"full-library":[178],"totals":[179],"were":[180],"restored.":[181],"This":[182],"corrected":[183],"one":[184],"denominator-dependent":[185],"result":[186],"refute":[190],"broader":[192],"concern;":[194],"nominal-level":[195],"unresolved.":[198],"therefore":[200],"contributes":[201],"multivariable":[203],"extension":[204],"together":[210],"explicit":[213],"account":[214],"where":[216],"its":[217],"inference":[218],"is":[219,264],"valid:":[220],"coefficients":[222],"are":[223],"supported":[224],"independent":[226],"biological":[227],"libraries,":[228],"whereas":[229],"summaries":[231],"partitioned-bin":[233],"designs":[234,257],"require":[235],"correlation-aware":[236],"or":[238],"joint":[239],"modelling":[240],"present":[243],"implementation":[244],"provides":[245],"diagnostically":[246],"generatively.":[249],"We":[250],"report":[251],"boundary":[253],"because":[254,262],"complex":[255],"pooled":[256],"make":[258],"it":[259,263],"consequential,":[260],"unique":[265],"model.":[269]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-02T00:00:00"}
