{"id":"https://openalex.org/W4402164248","doi":"https://doi.org/10.1186/s13040-024-00380-2","title":"Seven quick tips for gene-focused computational pangenomic analysis","display_name":"Seven quick tips for gene-focused computational pangenomic analysis","publication_year":2024,"publication_date":"2024-09-03","ids":{"openalex":"https://openalex.org/W4402164248","doi":"https://doi.org/10.1186/s13040-024-00380-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/39227987"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-024-00380-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00380-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00380-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00380-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058658234","display_name":"Vincenzo Bonnici","orcid":"https://orcid.org/0000-0002-1637-7545"},"institutions":[{"id":"https://openalex.org/I124601658","display_name":"University of Parma","ror":"https://ror.org/02k7wn190","country_code":"IT","type":"education","lineage":["https://openalex.org/I124601658"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Vincenzo Bonnici","raw_affiliation_strings":["Dipartimento di Scienze Matematiche Fisiche e Informatiche, Universit\u00e0\u00a0di\u00a0Parma, Parma, Italy. vincenzo.bonnici@unipr.it"],"raw_orcid":"https://orcid.org/0000-0002-1637-7545","affiliations":[{"raw_affiliation_string":"Dipartimento di Scienze Matematiche Fisiche e Informatiche, Universit\u00e0\u00a0di\u00a0Parma, Parma, Italy. vincenzo.bonnici@unipr.it","institution_ids":["https://openalex.org/I124601658"]}]},{"author_position":"last","author":{"id":null,"display_name":"Davide Chicco","orcid":"https://orcid.org/0000-0002-6279-6660"},"institutions":[{"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"]},{"id":"https://openalex.org/I4210140564","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Milano Bicocca","ror":"https://ror.org/03xejxm22","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210140564"]},{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["CA","IT"],"is_corresponding":false,"raw_author_name":"Davide Chicco","raw_affiliation_strings":["Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0\u00a0di\u00a0Milano-Bicocca, Milan, Italy. davidechicco@davidechicco.it","Institute of Health Policy Management and Evaluation, University\u00a0of\u00a0Toronto, Toronto, Ontario, Canada. davidechicco@davidechicco.it"],"raw_orcid":"https://orcid.org/0000-0002-6279-6660","affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica Sistemistica e Comunicazione, Universit\u00e0\u00a0di\u00a0Milano-Bicocca, Milan, Italy. davidechicco@davidechicco.it","institution_ids":["https://openalex.org/I66752286","https://openalex.org/I4210140564"]},{"raw_affiliation_string":"Institute of Health Policy Management and Evaluation, University\u00a0of\u00a0Toronto, Toronto, Ontario, Canada. davidechicco@davidechicco.it","institution_ids":["https://openalex.org/I185261750"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5058658234"],"corresponding_institution_ids":["https://openalex.org/I124601658"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.15,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.9165701,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"28","last_page":"28"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9925000071525574,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.665974497795105},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3949997127056122},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3647349178791046},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3223276734352112},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14964869618415833}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.665974497795105},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3949997127056122},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3647349178791046},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3223276734352112},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14964869618415833}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13040-024-00380-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00380-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00380-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:39227987","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39227987","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":"BioData mining","raw_type":null},{"id":"pmh:oai:boa.unimib.it:10281/515980","is_oa":true,"landing_page_url":"https://hdl.handle.net/10281/515980","pdf_url":"https://boa.unimib.it/bitstream/10281/515980/1/Bonnici-Chicco-2024-BioData%20Mining-VoR.pdf","source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11370085","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11370085","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11370085/pdf/13040_2024_Article_380.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:89cd64c88a384513b17f51cd500af8be","is_oa":true,"landing_page_url":"https://doaj.org/article/89cd64c88a384513b17f51cd500af8be","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 17, Iss 1, Pp 1-14 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-024-00380-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00380-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00380-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322275","display_name":"Universit\u00e0 degli Studi di Trento","ror":"https://ror.org/05trd4x28"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402164248.pdf","grobid_xml":"https://content.openalex.org/works/W4402164248.grobid-xml"},"referenced_works_count":90,"referenced_works":["https://openalex.org/W84733630","https://openalex.org/W1488857502","https://openalex.org/W1849979647","https://openalex.org/W1958058086","https://openalex.org/W1968298460","https://openalex.org/W1972859727","https://openalex.org/W1973094248","https://openalex.org/W1983793185","https://openalex.org/W2015292449","https://openalex.org/W2020541351","https://openalex.org/W2041267682","https://openalex.org/W2055615325","https://openalex.org/W2069375590","https://openalex.org/W2072876893","https://openalex.org/W2079213755","https://openalex.org/W2093610003","https://openalex.org/W2096093282","https://openalex.org/W2099521715","https://openalex.org/W2100471807","https://openalex.org/W2100874222","https://openalex.org/W2110397906","https://openalex.org/W2112506613","https://openalex.org/W2121055398","https://openalex.org/W2122673596","https://openalex.org/W2123006317","https://openalex.org/W2125119899","https://openalex.org/W2138434519","https://openalex.org/W2141735861","https://openalex.org/W2142678478","https://openalex.org/W2143485490","https://openalex.org/W2145100181","https://openalex.org/W2150550043","https://openalex.org/W2165446840","https://openalex.org/W2191243614","https://openalex.org/W2237956683","https://openalex.org/W2302501749","https://openalex.org/W2340958225","https://openalex.org/W2497052028","https://openalex.org/W2571294499","https://openalex.org/W2606519017","https://openalex.org/W2733722625","https://openalex.org/W2736848882","https://openalex.org/W2745006471","https://openalex.org/W2765745983","https://openalex.org/W2782546270","https://openalex.org/W2808718576","https://openalex.org/W2913484091","https://openalex.org/W2942967593","https://openalex.org/W2949102320","https://openalex.org/W2950336271","https://openalex.org/W2950891420","https://openalex.org/W2969556636","https://openalex.org/W3006570802","https://openalex.org/W3009070426","https://openalex.org/W3012393121","https://openalex.org/W3021348214","https://openalex.org/W3043408355","https://openalex.org/W3045244624","https://openalex.org/W3047585652","https://openalex.org/W3047903919","https://openalex.org/W3084380827","https://openalex.org/W3115101262","https://openalex.org/W3135022255","https://openalex.org/W3200776886","https://openalex.org/W3202751523","https://openalex.org/W3212967084","https://openalex.org/W4220680041","https://openalex.org/W4220895458","https://openalex.org/W4220985791","https://openalex.org/W4221118509","https://openalex.org/W4249954951","https://openalex.org/W4253759977","https://openalex.org/W4280583823","https://openalex.org/W4283643410","https://openalex.org/W4285247394","https://openalex.org/W4286499349","https://openalex.org/W4290973443","https://openalex.org/W4290973528","https://openalex.org/W4293657072","https://openalex.org/W4295514274","https://openalex.org/W4296776309","https://openalex.org/W4311070988","https://openalex.org/W4360828777","https://openalex.org/W4362660695","https://openalex.org/W4376133202","https://openalex.org/W4385264521","https://openalex.org/W4385741486","https://openalex.org/W4388093235","https://openalex.org/W4388927384","https://openalex.org/W6629190851"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Pangenomics":[0],"is":[1],"a":[2,16,114,126],"relatively":[3],"new":[4],"scientific":[5],"field":[6,60],"which":[7],"investigates":[8],"the":[9,13,26,55,72,92,152],"union":[10],"of":[11,15,32],"all":[12],"genomes":[14,31,42],"clade.":[17],"The":[18],"word":[19],"pan":[20],"means":[21],"everything":[22],"in":[23,143],"ancient":[24],"Greek;":[25],"term":[27],"pangenomics":[28,52,88],"originally":[29],"regarded":[30],"bacteria":[33],"and":[34,97,120,137,157,161],"was":[35],"later":[36],"intended":[37],"to":[38,40,50,57,81,87,94,98,135,141,162],"refer":[39],"human":[41],"as":[43],"well.":[44],"Modern":[45],"bioinformatics":[46,73],"offers":[47],"several":[48],"tools":[49],"analyze":[51],"data,":[53],"paving":[54],"way":[56],"an":[58],"emerging":[59],"that":[61],"we":[62,111],"can":[63,150],"call":[64],"computational":[65,68,77,122],"pangenomics.":[66],"Current":[67],"power":[69],"available":[70],"for":[71,118],"community":[74],"has":[75],"made":[76],"pangenomic":[78,123,159],"analyses":[79,124,160],"easy":[80],"perform,":[82],"but":[83],"this":[84,109,144],"higher":[85],"accessibility":[86],"analysis":[89],"also":[90],"increases":[91],"chances":[93],"make":[95],"mistakes":[96,134],"produce":[99],"misleading":[100],"or":[101],"inflated":[102],"results,":[103],"especially":[104],"by":[105,131],"beginners.":[106],"To":[107],"handle":[108],"problem,":[110],"present":[112],"here":[113],"few":[115],"quick":[116],"tips":[117],"efficient":[119],"correct":[121],"with":[125],"focus":[127],"on":[128],"bacterial":[129],"pangenomics,":[130],"describing":[132],"common":[133],"avoid":[136],"experienced":[138],"best":[139],"practices":[140],"follow":[142],"field.":[145],"We":[146],"believe":[147],"our":[148],"recommendations":[149],"help":[151],"readers":[153],"perform":[154],"more":[155,164],"robust":[156],"sound":[158],"generate":[163],"reliable":[165],"results.":[166]},"counts_by_year":[{"year":2025,"cited_by_count":5}],"updated_date":"2026-03-12T06:13:28.667946","created_date":"2025-10-10T00:00:00"}
