{"id":"https://openalex.org/W2091527062","doi":"https://doi.org/10.1186/s12859-015-0479-2","title":"A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium","display_name":"A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium","publication_year":2015,"publication_date":"2015-02-21","ids":{"openalex":"https://openalex.org/W2091527062","doi":"https://doi.org/10.1186/s12859-015-0479-2","mag":"2091527062","pmid":"https://pubmed.ncbi.nlm.nih.gov/25887316"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0479-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0479-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0479-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0479-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064864858","display_name":"Juan P. Steibel","orcid":"https://orcid.org/0000-0003-1725-2389"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Juan P Steibel","raw_affiliation_strings":["Department of Animal Science, Michigan State University, East Lansing MI, 48824, USA. steibelj@msu.edu","Department of Animal Science, Michigan State University, East Lansing MI, 48824, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Animal Science, Michigan State University, East Lansing MI, 48824, USA. steibelj@msu.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Animal Science, Michigan State University, East Lansing MI, 48824, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100453950","display_name":"Heng Wang","orcid":"https://orcid.org/0000-0002-1727-9226"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heng Wang","raw_affiliation_strings":["Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing MI, 48824, USA. hengwang@stt.msu.edu","Lyman Briggs College, Michigan State University, East Lansing MI, 48824, USA. hengwang@stt.msu.edu","Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing MI, 48824, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing MI, 48824, USA. hengwang@stt.msu.edu","institution_ids":[]},{"raw_affiliation_string":"Lyman Briggs College, Michigan State University, East Lansing MI, 48824, USA. hengwang@stt.msu.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing MI, 48824, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103799852","display_name":"Ping-Shou Zhong","orcid":null},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ping-Shou Zhong","raw_affiliation_strings":["Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing MI, 48824, USA. pszhong@stt.msu.edu","Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing MI, 48824, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing MI, 48824, USA. pszhong@stt.msu.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing MI, 48824, USA","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5064864858"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.05662458,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"16","issue":"1","first_page":"61","last_page":"61"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.8553000092506409,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.8553000092506409,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.02160000056028366,"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/T10885","display_name":"Gene expression and cancer classification","score":0.01940000057220459,"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/hidden-markov-model","display_name":"Hidden Markov model","score":0.7613974809646606},{"id":"https://openalex.org/keywords/linkage-disequilibrium","display_name":"Linkage disequilibrium","score":0.7196882963180542},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.6617809534072876},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.639171838760376},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.56456458568573},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4944112300872803},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.45690762996673584},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4442817270755768},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.415426105260849},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3015255331993103},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2578623294830322},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2514588236808777}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.7613974809646606},{"id":"https://openalex.org/C35605836","wikidata":"https://www.wikidata.org/wiki/Q2064311","display_name":"Linkage disequilibrium","level":5,"score":0.7196882963180542},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.6617809534072876},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.639171838760376},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.56456458568573},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4944112300872803},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.45690762996673584},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4442817270755768},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.415426105260849},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3015255331993103},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2578623294830322},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2514588236808777}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022981","descriptor_name":"Allelic Imbalance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022981","descriptor_name":"Allelic Imbalance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022981","descriptor_name":"Allelic Imbalance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-015-0479-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0479-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0479-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25887316","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25887316","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,"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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3318167","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4351697","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0479-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0479-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0479-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2416077190","display_name":"Collaborative Research:  High Dimensional Multivariate Analysis","funder_award_id":"1309156","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2721643973","display_name":"Statistical inference for gene regulation with genetical genomic data","funder_award_id":"1209112","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5429253674","display_name":null,"funder_award_id":"2010-65205-20342","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G5955074526","display_name":null,"funder_award_id":"DMS-1209112","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G824977163","display_name":null,"funder_award_id":"DMS-1309156","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321390","display_name":"Fonds De La Recherche Scientifique - FNRS","ror":"https://ror.org/03q83t159"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2091527062.pdf","grobid_xml":"https://content.openalex.org/works/W2091527062.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1968668741","https://openalex.org/W1972088832","https://openalex.org/W1977055616","https://openalex.org/W1978877986","https://openalex.org/W1981509058","https://openalex.org/W2002252353","https://openalex.org/W2005287518","https://openalex.org/W2021828797","https://openalex.org/W2025302103","https://openalex.org/W2027455260","https://openalex.org/W2034441254","https://openalex.org/W2035997482","https://openalex.org/W2039585509","https://openalex.org/W2048333131","https://openalex.org/W2049576543","https://openalex.org/W2049633694","https://openalex.org/W2053600267","https://openalex.org/W2063311473","https://openalex.org/W2065776802","https://openalex.org/W2086699924","https://openalex.org/W2092645627","https://openalex.org/W2097065948","https://openalex.org/W2100640908","https://openalex.org/W2104570606","https://openalex.org/W2108234281","https://openalex.org/W2114104545","https://openalex.org/W2118960339","https://openalex.org/W2121150886","https://openalex.org/W2125838338","https://openalex.org/W2129916363","https://openalex.org/W2133812303","https://openalex.org/W2134199796","https://openalex.org/W2138345444","https://openalex.org/W2149681218","https://openalex.org/W2150131459","https://openalex.org/W2154634293","https://openalex.org/W2160717298","https://openalex.org/W2161815151","https://openalex.org/W2168133698","https://openalex.org/W2170551349"],"related_works":["https://openalex.org/W2389124870","https://openalex.org/W2378369506","https://openalex.org/W2391803837","https://openalex.org/W4361273069","https://openalex.org/W2093214227","https://openalex.org/W2039373331","https://openalex.org/W2069461486","https://openalex.org/W2473486371","https://openalex.org/W2102796473","https://openalex.org/W2410452464"],"abstract_inverted_index":{"BACKGROUND:":[0],"Allelic":[1],"specific":[2],"expression":[3,14],"(ASE)":[4],"increases":[5],"our":[6],"understanding":[7],"of":[8,12,30,34,40,49,108,112,169,243,258,307,325],"the":[9,50,58,106,110,123,129,147,158,172,178,187,199,219,233,244,256,259,278,288,305,317,329],"genetic":[10,260],"control":[11,198],"gene":[13],"and":[15,87,116,127,177,225,237,246,262,275,280,309],"its":[16],"links":[17],"to":[18,65,99,132,141,151,241,272,283,322],"phenotypic":[19],"variation.":[20],"ASE":[21,75,139,148,184,263,279,308,326,338],"testing":[22],"is":[23,149,185,320],"implemented":[24],"through":[25],"binomial":[26],"or":[27,91],"beta-binomial":[28],"tests":[29],"sequence":[31,72,292],"read":[32],"counts":[33],"alternative":[35],"alleles":[36],"at":[37,204],"a":[38,162,190,205,213,315],"cSNP":[39,51,301],"interest":[41],"in":[42,97,167,228,304],"heterozygous":[43,230,330],"individuals.":[44,55],"This":[45],"requires":[46],"prior":[47],"ascertainment":[48],"genotypes":[52,111,251,302],"for":[53,255,277,300,328,337],"all":[54],"To":[56],"meet":[57],"needs,":[59],"we":[60],"propose":[61,80],"hidden":[62,82],"Markov":[63,83],"methods":[64,221],"call":[66,285,299],"SNPs":[67,114,126,231,286],"from":[68,287],"next":[69,289],"generation":[70,290],"RNA":[71,291],"data":[73,215],"when":[74,146],"possibly":[76],"exists.":[77],"RESULTS:":[78],"We":[79,266],"two":[81],"models":[84],"(HMMs),":[85],"HMM-ASE":[86,137,188],"HMM-NASE":[88],"that":[89,157,218,242],"consider":[90,94],"do":[92],"not":[93],"ASE,":[95],"respectively,":[96,121],"order":[98],"improve":[100,143],"genotyping":[101],"accuracy.":[102],"Both":[103],"HMMs":[104,159],"have":[105,222],"advantages":[107],"calling":[109,229],"several":[113],"simultaneously":[115,284],"allow":[117],"mapping":[118,133,281],"error":[119],"which,":[120],"utilize":[122],"dependence":[124],"among":[125],"correct":[128],"bias":[130],"due":[131],"error.":[134],"In":[135],"addition,":[136],"exploits":[138],"information":[140],"further":[142],"genotype":[144],"accuracy":[145,166],"likely":[150],"be":[152,335],"present.":[153],"Simulation":[154],"results":[155],"indicate":[156],"proposed":[160,220,318],"demonstrate":[161,217],"very":[163],"good":[164,253],"prediction":[165],"terms":[168],"controlling":[170],"both":[171,196],"false":[173,179,200],"discovery":[174,201],"rate":[175,181,202],"(FDR)":[176,203],"negative":[180],"(FNR).":[182],"When":[183],"present,":[186],"had":[189],"lower":[191],"FNR":[192],"than":[193,232],"HMM-NASE,":[194],"while":[195],"can":[197,297,333],"similar":[206,226,240],"level.":[207],"By":[208],"exploiting":[209],"linkage":[210],"disequilibrium":[211],"(LD),":[212],"real":[214],"application":[216],"better":[223],"sensitivity":[224],"FDR":[227,238],"VarScan":[234],"method.":[235],"Sensitivity":[236],"are":[239,270],"BCFtools":[245],"Beagle":[247],"methods.":[248],"The":[249,294],"resulting":[250],"show":[252],"properties":[254],"estimation":[257],"parameters":[261],"ratios.":[264],"CONCLUSIONS:":[265],"introduce":[267],"HMMs,":[268],"which":[269,332],"able":[271,321],"exploit":[273],"LD":[274],"account":[276],"errors,":[282],"data.":[293],"method":[295,319],"introduced":[296],"reliably":[298],"even":[303],"presence":[306],"under":[310],"low":[311],"sequencing":[312],"coverage.":[313],"As":[314],"byproduct,":[316],"provide":[323],"predictions":[324],"ratios":[327],"genotypes,":[331],"then":[334],"used":[336],"testing.":[339]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}