{"id":"https://openalex.org/W2031992856","doi":"https://doi.org/10.1186/1748-7188-4-2","title":"CHSMiner: a GUI tool to identify chromosomal homologous segments","display_name":"CHSMiner: a GUI tool to identify chromosomal homologous segments","publication_year":2009,"publication_date":"2009-01-15","ids":{"openalex":"https://openalex.org/W2031992856","doi":"https://doi.org/10.1186/1748-7188-4-2","mag":"2031992856","pmid":"https://pubmed.ncbi.nlm.nih.gov/19146671"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-4-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-4-2","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-4-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-4-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100422304","display_name":"Zhen Wang","orcid":"https://orcid.org/0000-0002-1695-4517"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Wang","raw_affiliation_strings":["Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, PR China. zwang01@sibs.ac.cn","Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, PR China. zwang01@sibs.ac.cn","institution_ids":["https://openalex.org/I4210106477"]},{"raw_affiliation_string":"Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, PR China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076249394","display_name":"Guohui Ding","orcid":"https://orcid.org/0000-0002-2888-1335"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I4210123885","display_name":"Shanghai Institute of Applied Physics","ror":"https://ror.org/02w6gr951","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210123885"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guohui Ding","raw_affiliation_strings":["Graduate School of the Chinese Academy of Sciences, Shanghai, 200031, PR China","Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of the Chinese Academy of Sciences, Shanghai, 200031, PR China","institution_ids":["https://openalex.org/I4210123885"]},{"raw_affiliation_string":"Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, PR China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112258190","display_name":"Zhonghao Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhonghao Yu","raw_affiliation_strings":["College of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115602441","display_name":"Lei Liu","orcid":"https://orcid.org/0000-0002-4604-4629"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lei Liu","raw_affiliation_strings":["Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, PR China","Shanghai Centre for Bioinformation Technology, 100 Qinzhou Road, Shanghai, 200235, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, PR China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Shanghai Centre for Bioinformation Technology, 100 Qinzhou Road, Shanghai, 200235, PR China","institution_ids":["https://openalex.org/I4210162648"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008280608","display_name":"Yixue Li","orcid":"https://orcid.org/0000-0002-1198-7176"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yixue Li","raw_affiliation_strings":["College of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China","Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, PR China","Shanghai Centre for Bioinformation Technology, 100 Qinzhou Road, Shanghai, 200235, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, PR China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Shanghai Centre for Bioinformation Technology, 100 Qinzhou Road, Shanghai, 200235, PR China","institution_ids":["https://openalex.org/I4210162648"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5008280608","https://openalex.org/A5115602441"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I19820366","https://openalex.org/I4210106477","https://openalex.org/I4210162648"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.9494,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.78426205,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"4","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.3637999892234802,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.3637999892234802,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.3003999888896942,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.2134999930858612,"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/computer-science","display_name":"Computer science","score":0.6341942548751831},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.4438643157482147},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4242396056652069},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27189862728118896},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2331024706363678},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14820653200149536}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6341942548751831},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.4438643157482147},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4242396056652069},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27189862728118896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2331024706363678},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14820653200149536}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1748-7188-4-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-4-2","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-4-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:19146671","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19146671","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:b51270ccaf084fe588470a6ab6e2f569","is_oa":false,"landing_page_url":"https://doaj.org/article/b51270ccaf084fe588470a6ab6e2f569","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 4, Iss 1, p 2 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2647922","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2647922","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":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-4-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-4-2","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-4-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2031992856.pdf","grobid_xml":"https://content.openalex.org/works/W2031992856.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1969260677","https://openalex.org/W1973788898","https://openalex.org/W1976245710","https://openalex.org/W2011889195","https://openalex.org/W2026055857","https://openalex.org/W2038035134","https://openalex.org/W2048009853","https://openalex.org/W2097710447","https://openalex.org/W2112118427","https://openalex.org/W2127295545","https://openalex.org/W2128207225","https://openalex.org/W2143790738","https://openalex.org/W2151302772","https://openalex.org/W2166589098","https://openalex.org/W4210241463"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"identification":[2],"of":[3,27,64,117],"chromosomal":[4],"homologous":[5],"segments":[6],"(CHS)":[7],"within":[8],"and":[9,21,52,56,74,78,86,99,109,115],"between":[10],"genomes":[11],"is":[12,91],"essential":[13],"for":[14,106],"comparative":[15],"genomics.":[16],"Various":[17],"processes":[18],"including":[19],"insertion/deletion":[20],"inversion":[22],"could":[23],"cause":[24],"the":[25,65,69,113],"degeneration":[26],"CHSs.":[28],"RESULTS:":[29],"Here":[30],"we":[31],"present":[32],"a":[33],"Java":[34],"software":[35,70,85],"CHSMiner":[36,90],"that":[37],"detects":[38],"CHSs":[39],"based":[40],"on":[41,71],"shared":[42],"gene":[43],"content":[44],"alone.":[45],"It":[46,102],"implements":[47],"fast":[48,97],"greedy":[49],"search":[50],"algorithm":[51],"rigorous":[53],"statistical":[54],"validation,":[55],"its":[57,80,94],"friendly":[58],"graphical":[59],"interface":[60],"allows":[61],"interactive":[62],"visualization":[63],"results.":[66],"We":[67],"tested":[68],"both":[72,107],"simulated":[73],"biological":[75],"realistic":[76],"data":[77,87],"compared":[79],"performance":[81],"with":[82],"similar":[83],"existing":[84],"source.":[88],"CONCLUSION:":[89],"characterized":[92],"by":[93],"integrated":[95],"workflow,":[96],"speed":[98],"convenient":[100],"usage.":[101],"will":[103],"be":[104],"useful":[105],"experimentalists":[108],"bioinformaticians":[110],"interested":[111],"in":[112],"structure":[114],"evolution":[116],"genomes.":[118]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
