{"id":"https://openalex.org/W4366083153","doi":"https://doi.org/10.1093/bioinformatics/btad188","title":"Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping","display_name":"Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping","publication_year":2023,"publication_date":"2023-04-01","ids":{"openalex":"https://openalex.org/W4366083153","doi":"https://doi.org/10.1093/bioinformatics/btad188","pmid":"https://pubmed.ncbi.nlm.nih.gov/37067484"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad188","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad188","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad188/49989157/btad188.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad188/49989157/btad188.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075933094","display_name":"Xiaoliang Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I4210101167","display_name":"Institute of Oceanology","ror":"https://ror.org/018yw5541","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210101167"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoliang Ren","raw_affiliation_strings":["Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071, China"],"affiliations":[{"raw_affiliation_string":"Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071, China","institution_ids":["https://openalex.org/I4210101167"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101745441","display_name":"Yanwen Shao","orcid":"https://orcid.org/0009-0002-4863-3504"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yanwen Shao","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115603686","display_name":"Yiwen Zhang","orcid":"https://orcid.org/0000-0003-1711-6870"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yiwen Zhang","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101487552","display_name":"Ying Ni","orcid":"https://orcid.org/0000-0002-6814-3476"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ying Ni","raw_affiliation_strings":["Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong , Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong , Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073101813","display_name":"Yu Bi","orcid":"https://orcid.org/0000-0003-2154-400X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yu Bi","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003632285","display_name":"Runsheng Li","orcid":"https://orcid.org/0000-0003-1563-1844"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"id":"https://openalex.org/I4210106122","display_name":"Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)","ror":"https://ror.org/00y7mag53","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210106122"]}],"countries":["CN","HK"],"is_corresponding":true,"raw_author_name":"Runsheng Li","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China","Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) , Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) , Guangzhou, China","institution_ids":["https://openalex.org/I4210106122"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5003632285"],"corresponding_institution_ids":["https://openalex.org/I168719708","https://openalex.org/I4210106122"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4525,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.66051597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"39","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9948999881744385,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9948999881744385,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9944999814033508,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6500404477119446},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6487510800361633},{"id":"https://openalex.org/keywords/primer","display_name":"Primer (cosmetics)","score":0.6228848695755005},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4340866506099701},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.43184882402420044},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3395780026912689},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3239133059978485},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.28034308552742004},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.19301649928092957}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6500404477119446},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6487510800361633},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.6228848695755005},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4340866506099701},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.43184882402420044},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3395780026912689},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3239133059978485},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.28034308552742004},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.19301649928092957},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad188","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad188","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad188/49989157/btad188.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37067484","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37067484","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10121334","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10121334","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10121334/pdf/btad188.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/ca1372b3-37d0-4c43-9d59-5137c5f5fda2","is_oa":true,"landing_page_url":"https://hdl.handle.net/2031/ca1372b3-37d0-4c43-9d59-5137c5f5fda2","pdf_url":null,"source":{"id":"https://openalex.org/S7407055387","display_name":"CityU Scholars","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Ren, X, Shao, Y, Zhang, Y, Ni, Y, Bi, Y & Li, R 2023, 'Primerdiffer : a python command-line module for large-scale primer design in haplotype genotyping', Bioinformatics, vol. 39, no. 4, btad188. https://doi.org/10.1093/bioinformatics/btad188","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad188","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad188","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad188/49989157/btad188.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4000000059604645,"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8"}],"awards":[{"id":"https://openalex.org/G1223952294","display_name":null,"funder_award_id":"9610497","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320330495","display_name":"Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)","ror":"https://ror.org/00y7mag53"},{"id":"https://openalex.org/F4320335055","display_name":"Health and Medical Research Fund","ror":"https://ror.org/03qh32912"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4366083153.pdf"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1981222811","https://openalex.org/W2009119978","https://openalex.org/W2032019813","https://openalex.org/W2066852475","https://openalex.org/W2131463690","https://openalex.org/W2162098634","https://openalex.org/W2163910672","https://openalex.org/W2169486828","https://openalex.org/W2943577714"],"related_works":["https://openalex.org/W2529681551","https://openalex.org/W1965396974","https://openalex.org/W2002128513","https://openalex.org/W2038331681","https://openalex.org/W1983642025","https://openalex.org/W1998686087","https://openalex.org/W2066137273","https://openalex.org/W2044943383","https://openalex.org/W2092874662","https://openalex.org/W1981169569"],"abstract_inverted_index":{"The":[0],"open-source":[1],"python":[2],"modules":[3],"are":[4],"available":[5],"at":[6],"github":[7],"(https://github.com/runsheng/primerdiffer,":[8],"https://github.com/runsheng/primervcf)":[9],"and":[10],"Python":[11],"package":[12],"index":[13],"(https://pypi.org/project/primerdiffer/,":[14],"https://pypi.org/project/primervcf/).":[15]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-19T08:26:33.389920","created_date":"2025-10-10T00:00:00"}
