{"id":"https://openalex.org/W2070791418","doi":"https://doi.org/10.1186/1471-2105-13-206","title":"CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes","display_name":"CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes","publication_year":2012,"publication_date":"2012-08-17","ids":{"openalex":"https://openalex.org/W2070791418","doi":"https://doi.org/10.1186/1471-2105-13-206","mag":"2070791418","pmid":"https://pubmed.ncbi.nlm.nih.gov/22901030"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-206","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-206","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-206","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/10.1186/1471-2105-13-206","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031128952","display_name":"Ivan Borozan","orcid":"https://orcid.org/0000-0002-3145-3550"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ivan Borozan","raw_affiliation_strings":["Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada","Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I112260969"]},{"raw_affiliation_string":"Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada","institution_ids":["https://openalex.org/I112260969"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078772433","display_name":"Shane Wilson","orcid":null},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shane Wilson","raw_affiliation_strings":["Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada","institution_ids":["https://openalex.org/I112260969"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053546523","display_name":"Paola Blanchette","orcid":null},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Paola Blanchette","raw_affiliation_strings":["Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088024384","display_name":"Philippe Laflamme","orcid":null},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Philippe Laflamme","raw_affiliation_strings":["Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada","institution_ids":["https://openalex.org/I112260969"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032150107","display_name":"Stuart Watt","orcid":"https://orcid.org/0000-0002-6749-3474"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Stuart N Watt","raw_affiliation_strings":["Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada","institution_ids":["https://openalex.org/I112260969"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045117915","display_name":"Paul M. Krzyzanowski","orcid":"https://orcid.org/0000-0001-6430-5995"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Paul M Krzyzanowski","raw_affiliation_strings":["Ontario Cancer Institute and the Campbell Family Cancer Research Institute, Toronto Medical Discovery Tower, University of Toronto, 101 College Street, Rm 8-703, Toronto, Ontario, M5G 1L7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Cancer Institute and the Campbell Family Cancer Research Institute, Toronto Medical Discovery Tower, University of Toronto, 101 College Street, Rm 8-703, Toronto, Ontario, M5G 1L7, Canada","institution_ids":["https://openalex.org/I112260969","https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040543550","display_name":"Fabrice Sircoulomb","orcid":"https://orcid.org/0000-0002-9300-5905"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Fabrice Sircoulomb","raw_affiliation_strings":["Ontario Cancer Institute and the Campbell Family Cancer Research Institute, Toronto Medical Discovery Tower, University of Toronto, 101 College Street, Rm 8-703, Toronto, Ontario, M5G 1L7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Cancer Institute and the Campbell Family Cancer Research Institute, Toronto Medical Discovery Tower, University of Toronto, 101 College Street, Rm 8-703, Toronto, Ontario, M5G 1L7, Canada","institution_ids":["https://openalex.org/I112260969","https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090218407","display_name":"Robert Rottapel","orcid":"https://orcid.org/0000-0002-6024-5558"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Robert Rottapel","raw_affiliation_strings":["Ontario Cancer Institute and the Campbell Family Cancer Research Institute, Toronto Medical Discovery Tower, University of Toronto, 101 College Street, Rm 8-703, Toronto, Ontario, M5G 1L7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Cancer Institute and the Campbell Family Cancer Research Institute, Toronto Medical Discovery Tower, University of Toronto, 101 College Street, Rm 8-703, Toronto, Ontario, M5G 1L7, Canada","institution_ids":["https://openalex.org/I112260969","https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057466781","display_name":"Philip E. Branton","orcid":null},"institutions":[{"id":"https://openalex.org/I2801766832","display_name":"McGill University Health Centre","ror":"https://ror.org/04cpxjv19","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801766832"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Philip E Branton","raw_affiliation_strings":["Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada","Department of Oncology, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada","The Goodman Cancer Research Centre, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Department of Oncology, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"The Goodman Cancer Research Centre, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada","institution_ids":["https://openalex.org/I2801766832"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042826125","display_name":"Vincent Ferretti","orcid":"https://orcid.org/0000-0002-2555-1277"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Vincent Ferretti","raw_affiliation_strings":["Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada","institution_ids":["https://openalex.org/I112260969"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5042826125"],"corresponding_institution_ids":["https://openalex.org/I112260969"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.9863,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.86230476,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"1","first_page":"206","last_page":"206"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.24199999868869781,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.24199999868869781,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.06679999828338623,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.04280000180006027,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7099076509475708},{"id":"https://openalex.org/keywords/capsid","display_name":"Capsid","score":0.6555976867675781},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6236884593963623},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6140240430831909},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.507445752620697},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.45930254459381104},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.4455111622810364},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.43148452043533325},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.42231106758117676},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.35220658779144287},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3479273319244385},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08059719204902649}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7099076509475708},{"id":"https://openalex.org/C202878990","wikidata":"https://www.wikidata.org/wiki/Q830465","display_name":"Capsid","level":3,"score":0.6555976867675781},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6236884593963623},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6140240430831909},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.507445752620697},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.45930254459381104},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.4455111622810364},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.43148452043533325},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.42231106758117676},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35220658779144287},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3479273319244385},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08059719204902649},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D009858","descriptor_name":"Oncogenic Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009858","descriptor_name":"Oncogenic Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009858","descriptor_name":"Oncogenic Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010051","descriptor_name":"Ovarian Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-13-206","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-206","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-206","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:22901030","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22901030","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:utoronto.scholaris.ca:1807/83095","is_oa":true,"landing_page_url":"http://hdl.handle.net/1807/83095","pdf_url":"https://utoronto.scholaris.ca/bitstreams/c0c9a70a-0c0a-453d-b60a-c9229e3678db/download","source":{"id":"https://openalex.org/S4306400261","display_name":"TSpace (University of Toronto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I185261750","host_organization_name":"University of Toronto","host_organization_lineage":["https://openalex.org/I185261750"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:fcdaf004bcce4c6195448112284a5fb9","is_oa":true,"landing_page_url":"https://doaj.org/article/fcdaf004bcce4c6195448112284a5fb9","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 13, Iss 1, p 206 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2463381","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3464663","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"},{"id":"pmh:oai:localhost:1807/83095","is_oa":false,"landing_page_url":"http://doi.org/10.1186/1471-2105-13-206","pdf_url":null,"source":{"id":"https://openalex.org/S4306400261","display_name":"TSpace (University of Toronto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I185261750","host_organization_name":"University of Toronto","host_organization_lineage":["https://openalex.org/I185261750"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-206","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-206","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-206","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":[{"id":"https://openalex.org/F4320313290","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54"},{"id":"https://openalex.org/F4320314607","display_name":"Government of Ontario","ror":"https://ror.org/015pzp858"},{"id":"https://openalex.org/F4320322597","display_name":"Terry Fox Research Institute","ror":"https://ror.org/05vd00053"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2070791418.pdf","grobid_xml":"https://content.openalex.org/works/W2070791418.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1496050929","https://openalex.org/W1981194976","https://openalex.org/W1988460088","https://openalex.org/W2044296969","https://openalex.org/W2055043387","https://openalex.org/W2082429669","https://openalex.org/W2085487956","https://openalex.org/W2098521327","https://openalex.org/W2107644675","https://openalex.org/W2108552490","https://openalex.org/W2114850508","https://openalex.org/W2115452925","https://openalex.org/W2121906867","https://openalex.org/W2124985265","https://openalex.org/W2126419817","https://openalex.org/W2126493747","https://openalex.org/W2127640118","https://openalex.org/W2136145671","https://openalex.org/W2140154634","https://openalex.org/W2142299476","https://openalex.org/W2160969485","https://openalex.org/W2165918134","https://openalex.org/W2167155938","https://openalex.org/W2167391272","https://openalex.org/W2168150091","https://openalex.org/W2199902421","https://openalex.org/W2478808649"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W4401246297","https://openalex.org/W2137572138","https://openalex.org/W4316495397","https://openalex.org/W4399812588","https://openalex.org/W2030680494","https://openalex.org/W2939973050","https://openalex.org/W4235011756","https://openalex.org/W2166777687","https://openalex.org/W2107233609"],"abstract_inverted_index":{"BACKGROUND:":[0],"It":[1],"is":[2,134],"now":[3],"well":[4],"established":[5],"that":[6,109],"nearly":[7],"20%":[8],"of":[9,20,32,60,123,153,161,176],"human":[10,21,55,178],"cancers":[11],"are":[12],"caused":[13],"by":[14,41],"infectious":[15],"agents,":[16],"and":[17,38,52,81,85,93,105,130,133,151,166,179],"the":[18,27,111,149,177,183,188],"list":[19],"oncogenic":[22],"pathogens":[23],"will":[24],"grow":[25],"in":[26,54,90,182,187,196],"future":[28],"for":[29,49,78,102,120],"a":[30,74,97,106,158,163],"variety":[31],"cancer":[33],"types.":[34],"Whole":[35],"tumor":[36,91],"transcriptome":[37,167],"genome":[39,112,131],"sequencing":[40,43],"next-generation":[42],"technologies":[44],"presents":[45],"an":[46],"unparalleled":[47],"opportunity":[48],"pathogen":[50,87,180],"detection":[51],"discovery":[53],"tissues":[56],"but":[57],"requires":[58],"development":[59],"new":[61],"genome-wide":[62],"bioinformatics":[63,76],"tools.":[64],"RESULTS:":[65],"Here":[66],"we":[67,155],"present":[68],"CaPSID":[69,95,115,172],"(Computational":[70],"Pathogen":[71],"Sequence":[72],"IDentification),":[73],"comprehensive":[75,159],"platform":[77],"identifying,":[79],"querying":[80],"visualizing":[82],"both":[83,162],"exogenous":[84],"endogenous":[86],"nucleotide":[88],"sequences":[89,181],"genomes":[92],"transcriptomes.":[94],"includes":[96],"scalable,":[98],"high":[99],"performance":[100],"database":[101],"data":[103],"storage":[104],"web":[107],"application":[108],"integrates":[110],"browser":[113],"JBrowse.":[114],"also":[116],"provides":[117],"useful":[118],"metrics":[119],"sequence":[121],"analysis":[122,160],"pre-aligned":[124],"BAM":[125],"files,":[126],"such":[127],"as":[128],"gene":[129],"coverage,":[132],"optimized":[135],"to":[136],"run":[137],"efficiently":[138],"on":[139],"multiprocessor":[140],"computers":[141],"with":[142],"low":[143],"memory":[144],"usage.":[145],"CONCLUSIONS:":[146],"To":[147],"demonstrate":[148],"usefulness":[150],"efficiency":[152],"CaPSID,":[154],"carried":[156],"out":[157],"simulated":[164,184],"dataset":[165,190],"samples":[168],"from":[169],"ovarian":[170,189],"cancer.":[171],"correctly":[173],"identified":[174],"all":[175],"dataset,":[185],"while":[186],"CaPSID's":[191],"predictions":[192],"were":[193],"successfully":[194],"validated":[195],"vitro.":[197]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}