{"id":"https://openalex.org/W1870866180","doi":"https://doi.org/10.1186/1471-2105-7-4","title":"Application of machine learning in SNP discovery","display_name":"Application of machine learning in SNP discovery","publication_year":2006,"publication_date":"2006-01-06","ids":{"openalex":"https://openalex.org/W1870866180","doi":"https://doi.org/10.1186/1471-2105-7-4","mag":"1870866180","pmid":"https://pubmed.ncbi.nlm.nih.gov/16398931"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-4","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/10.1186/1471-2105-7-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057242692","display_name":"Lakshmi K. Matukumalli","orcid":null},"institutions":[{"id":"https://openalex.org/I1336096307","display_name":"United States Department of Agriculture","ror":"https://ror.org/01na82s61","country_code":"US","type":"government","lineage":["https://openalex.org/I1336096307"]},{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]},{"id":"https://openalex.org/I4210125976","display_name":"Beltsville Agricultural Research Center","ror":"https://ror.org/03b08sh51","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210125976","https://openalex.org/I4210138094"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lakshmi K Matukumalli","raw_affiliation_strings":["Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, US Department of Agriculture, ARS, Beltsville, MD 20705, USA. lmatukum@gmu.edu","Bioinformatics and Computational Biology, George Mason University, Manassas, USA","US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, US Department of Agriculture, ARS, Beltsville, MD 20705, USA. lmatukum@gmu.edu","institution_ids":["https://openalex.org/I4210125976"]},{"raw_affiliation_string":"Bioinformatics and Computational Biology, George Mason University, Manassas, USA","institution_ids":["https://openalex.org/I162714631"]},{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, USA","institution_ids":["https://openalex.org/I1336096307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066154658","display_name":"John J. Grefenstette","orcid":"https://orcid.org/0000-0001-6180-5177"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John J Grefenstette","raw_affiliation_strings":["Bioinformatics and Computational Biology, George Mason University, Manassas, VA, 20110, USA","Bioinformatics and Computational Biology, George Mason University, Manassas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology, George Mason University, Manassas, VA, 20110, USA","institution_ids":["https://openalex.org/I162714631"]},{"raw_affiliation_string":"Bioinformatics and Computational Biology, George Mason University, Manassas, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061392503","display_name":"David L. Hyten","orcid":"https://orcid.org/0000-0001-6324-9389"},"institutions":[{"id":"https://openalex.org/I1336096307","display_name":"United States Department of Agriculture","ror":"https://ror.org/01na82s61","country_code":"US","type":"government","lineage":["https://openalex.org/I1336096307"]},{"id":"https://openalex.org/I4210125976","display_name":"Beltsville Agricultural Research Center","ror":"https://ror.org/03b08sh51","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210125976","https://openalex.org/I4210138094"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David L Hyten","raw_affiliation_strings":["US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA","US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA","institution_ids":["https://openalex.org/I4210125976"]},{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, USA","institution_ids":["https://openalex.org/I1336096307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053666010","display_name":"Ik\u2010Young Choi","orcid":"https://orcid.org/0000-0003-4168-0471"},"institutions":[{"id":"https://openalex.org/I1336096307","display_name":"United States Department of Agriculture","ror":"https://ror.org/01na82s61","country_code":"US","type":"government","lineage":["https://openalex.org/I1336096307"]},{"id":"https://openalex.org/I4210125976","display_name":"Beltsville Agricultural Research Center","ror":"https://ror.org/03b08sh51","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210125976","https://openalex.org/I4210138094"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ik-Young Choi","raw_affiliation_strings":["US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA","US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA","institution_ids":["https://openalex.org/I4210125976"]},{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, USA","institution_ids":["https://openalex.org/I1336096307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025125196","display_name":"Perry B. Cregan","orcid":null},"institutions":[{"id":"https://openalex.org/I1336096307","display_name":"United States Department of Agriculture","ror":"https://ror.org/01na82s61","country_code":"US","type":"government","lineage":["https://openalex.org/I1336096307"]},{"id":"https://openalex.org/I4210125976","display_name":"Beltsville Agricultural Research Center","ror":"https://ror.org/03b08sh51","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210125976","https://openalex.org/I4210138094"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Perry B Cregan","raw_affiliation_strings":["US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA","US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA","institution_ids":["https://openalex.org/I4210125976"]},{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, Beltsville, USA","institution_ids":["https://openalex.org/I1336096307"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028661370","display_name":"Curtis P. Van Tassell","orcid":"https://orcid.org/0000-0002-8416-2087"},"institutions":[{"id":"https://openalex.org/I1336096307","display_name":"United States Department of Agriculture","ror":"https://ror.org/01na82s61","country_code":"US","type":"government","lineage":["https://openalex.org/I1336096307"]},{"id":"https://openalex.org/I4210125976","display_name":"Beltsville Agricultural Research Center","ror":"https://ror.org/03b08sh51","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210125976","https://openalex.org/I4210138094"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Curtis P Van Tassell","raw_affiliation_strings":["US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, MD, 20705, USA","US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, MD, 20705, USA","institution_ids":["https://openalex.org/I4210125976"]},{"raw_affiliation_string":"US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, USA","institution_ids":["https://openalex.org/I1336096307"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5028661370"],"corresponding_institution_ids":["https://openalex.org/I1336096307","https://openalex.org/I4210125976"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":3.1455,"has_fulltext":true,"cited_by_count":57,"citation_normalized_percentile":{"value":0.91503298,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"7","issue":"1","first_page":"4","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.2273000031709671,"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":0.2273000031709671,"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/T13984","display_name":"Nutrition, Genetics, and Disease","score":0.08619999885559082,"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/T12571","display_name":"Soybean genetics and cultivation","score":0.07689999788999557,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5848698616027832},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5637452602386475},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.5519254207611084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4747091829776764},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.434525728225708},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4204910695552826},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3416798710823059},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33034753799438477},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24228110909461975},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.21678242087364197},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.0954291820526123},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09535440802574158},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07966235280036926}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5848698616027832},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5637452602386475},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.5519254207611084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4747091829776764},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.434525728225708},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4204910695552826},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3416798710823059},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33034753799438477},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24228110909461975},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.21678242087364197},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0954291820526123},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09535440802574158},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07966235280036926}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006720","descriptor_name":"Homozygote","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006720","descriptor_name":"Homozygote","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006720","descriptor_name":"Homozygote","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006720","descriptor_name":"Homozygote","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011237","descriptor_name":"Predictive Value of Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013025","descriptor_name":"Glycine max","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016324","descriptor_name":"Sequence Tagged Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016324","descriptor_name":"Sequence Tagged Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016324","descriptor_name":"Sequence Tagged Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016324","descriptor_name":"Sequence Tagged Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-7-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-4","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:16398931","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16398931","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:digitalcommons.unl.edu:agronomyfacpub-2213","is_oa":true,"landing_page_url":"https://digitalcommons.unl.edu/agronomyfacpub/1224","pdf_url":"https://digitalcommons.unl.edu/agronomyfacpub/1224","source":{"id":"https://openalex.org/S4306400577","display_name":"Lincoln (University of Nebraska)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114395901","host_organization_name":"University of Nebraska\u2013Lincoln","host_organization_lineage":["https://openalex.org/I114395901"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Department of Agronomy and Horticulture: Faculty Publications","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:9308a38f4b88488e870ee352ae038f76","is_oa":true,"landing_page_url":"https://doaj.org/article/9308a38f4b88488e870ee352ae038f76","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 7, Iss 1, p 4 (2006)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1955739","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1955739","pdf_url":null,"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,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-4","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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1870866180.pdf","grobid_xml":"https://content.openalex.org/works/W1870866180.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W32754319","https://openalex.org/W1528782506","https://openalex.org/W1971307410","https://openalex.org/W1978728974","https://openalex.org/W2019898130","https://openalex.org/W2058970027","https://openalex.org/W2074363252","https://openalex.org/W2097906839","https://openalex.org/W2109831613","https://openalex.org/W2116079122","https://openalex.org/W2123097295","https://openalex.org/W2124861078","https://openalex.org/W2125055259","https://openalex.org/W2135217050","https://openalex.org/W2135893370","https://openalex.org/W2145307001","https://openalex.org/W2150893872","https://openalex.org/W2166020074","https://openalex.org/W2491923582","https://openalex.org/W3131343862","https://openalex.org/W4248537472","https://openalex.org/W6608097372"],"related_works":["https://openalex.org/W3026696341","https://openalex.org/W2774988270","https://openalex.org/W2258604039","https://openalex.org/W3110294858","https://openalex.org/W2978670733","https://openalex.org/W3207994248","https://openalex.org/W3045558373","https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2966739945"],"abstract_inverted_index":{"BACKGROUND:":[0],"Single":[1],"nucleotide":[2],"polymorphisms":[3],"(SNP)":[4],"constitute":[5],"more":[6],"than":[7],"90%":[8],"of":[9,91,140,173,192,210,234,253],"the":[10,163,169,216,237,254,288],"genetic":[11],"variation,":[12],"and":[13,31,78,135,182,202,228,267,312,326,345],"hence":[14,268],"can":[15,307,329,346],"account":[16],"for":[17,199,204,249,272,292],"most":[18],"trait":[19],"differences":[20],"among":[21],"individuals":[22],"in":[23,70,93,126,313,343],"a":[24,46,89,97,220,231,284,303,317],"given":[25],"species.":[26],"Polymorphism":[27],"detection":[28,290],"software":[29,291,340],"PolyBayes":[30,53,136,181,185,229,266],"PolyPhred":[32],"give":[33],"high":[34,261],"false":[35,243,262],"positive":[36,186],"SNP":[37,98,115,143,153,194,263,353],"predictions":[38,201,264],"even":[39],"with":[40,168,177,206],"stringent":[41],"parameter":[42],"values.":[43],"We":[44],"developed":[45,282],"machine":[47,277],"learning":[48,278],"(ML)":[49,279],"method":[50,280],"to":[51,54,66,88,95,218,222,247,260,287,333],"augment":[52],"improve":[55],"its":[56],"prediction":[57,294],"accuracy.":[58],"ML":[59,83,164,214,227,238,305,327,338],"methods":[60],"have":[61,258],"also":[62,330],"been":[63],"successfully":[64],"applied":[65,87,332],"other":[67,273],"bioinformatics":[68],"problems":[69],"predicting":[71],"genes,":[72],"promoters,":[73],"transcription":[74],"factor":[75],"binding":[76],"sites":[77],"protein":[79],"structures.":[80],"RESULTS:":[81],"The":[82,109,184,251,296,322],"program":[84,239],"C4.5":[85],"was":[86,281],"set":[90,325],"features":[92],"order":[94],"build":[96],"classifier":[99,306],"from":[100,129,147,154,298],"training":[101,110,162],"data":[102,111,139,175],"based":[103],"on":[104,171],"human":[105,310],"expert":[106],"decisions":[107],"(True/False).":[108],"were":[112,144,157,197],"27,275":[113],"candidate":[114,142,193],"generated":[116,145,240],"by":[117,159,265],"sequencing":[118],"1973":[119],"STS":[120,150],"(sequence":[121],"tag":[122],"sites)":[123],"(12":[124],"Mb)":[125],"both":[127,155,226],"directions":[128],"6":[130],"diverse":[131],"homozygous":[132],"soybean":[133,255],"cultivars":[134],"analysis.":[137],"Test":[138],"18,390":[141],"similarly":[146],"1359":[148],"additional":[149],"(8":[151],"Mb).":[152],"sets":[156],"classified":[158],"experts.":[160,183],"After":[161],"classifier,":[165],"it":[166],"agreed":[167],"experts":[170],"97.3%":[172],"test":[174],"compared":[176,246],"7.8%":[178,198],"agreement":[179],"between":[180],"predictive":[187],"values":[188],"(PPV)":[189],"(i.e.,":[190],"fraction":[191],"being":[195,211],"real)":[196],"all":[200,334],"16.7%":[203],"those":[205],"100%":[207],"posterior":[208],"probability":[209],"real.":[212],"Using":[213],"improved":[215],"PPV":[217],"84.8%,":[219],"5-":[221],"10-fold":[223],"increase.":[224],"While":[225],"produced":[230],"similar":[232],"number":[233],"true":[235],"positives,":[236],"only":[241],"249":[242],"positives":[244],"as":[245,283],"16,955":[248],"PolyBayes.":[250],"complexity":[252],"genome":[256],"may":[257,270],"contributed":[259],"results":[269,297],"differ":[271],"genomes.":[274],"CONCLUSION:":[275],"A":[276],"supplementary":[285],"feature":[286,324],"polymorphism":[289,335],"improving":[293],"accuracies.":[295],"this":[299,314],"study":[300],"indicate":[301],"that":[302],"trained":[304],"significantly":[308],"reduce":[309],"intervention":[311],"case":[315],"achieved":[316],"5-10":[318],"fold":[319],"enhanced":[320],"productivity.":[321],"optimized":[323],"framework":[328],"be":[331,347],"discovery":[336,354],"software.":[337],"support":[339],"is":[341],"written":[342],"Perl":[344],"easily":[348],"integrated":[349],"into":[350],"an":[351],"existing":[352],"pipeline.":[355]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}