{"id":"https://openalex.org/W4391347928","doi":"https://doi.org/10.1186/s12859-024-05640-w","title":"PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes","display_name":"PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes","publication_year":2024,"publication_date":"2024-01-30","ids":{"openalex":"https://openalex.org/W4391347928","doi":"https://doi.org/10.1186/s12859-024-05640-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/38291430"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05640-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05640-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05640-w","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/s12859-024-05640-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062315437","display_name":"Abigail Glascock","orcid":"https://orcid.org/0000-0002-6919-2632"},"institutions":[{"id":"https://openalex.org/I4210121800","display_name":"Chan Zuckerberg Initiative (United States)","ror":"https://ror.org/02qenvm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210121800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Abigail Glascock","raw_affiliation_strings":["Chan Zuckerberg Biohub, San Francisco, CA, USA. abigail.glascock@czbiohub.org","Chan Zuckerberg Biohub, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chan Zuckerberg Biohub, San Francisco, CA, USA. abigail.glascock@czbiohub.org","institution_ids":["https://openalex.org/I4210121800"]},{"raw_affiliation_string":"Chan Zuckerberg Biohub, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210121800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010670462","display_name":"Eric Waltari","orcid":"https://orcid.org/0000-0001-6930-9645"},"institutions":[{"id":"https://openalex.org/I4210121800","display_name":"Chan Zuckerberg Initiative (United States)","ror":"https://ror.org/02qenvm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210121800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Waltari","raw_affiliation_strings":["Chan Zuckerberg Biohub, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chan Zuckerberg Biohub, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210121800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009243392","display_name":"Gytis Dudas","orcid":"https://orcid.org/0000-0002-0227-4158"},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Gytis Dudas","raw_affiliation_strings":["Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063545192","display_name":"Joan Wong","orcid":"https://orcid.org/0000-0002-7849-6320"},"institutions":[{"id":"https://openalex.org/I4210121800","display_name":"Chan Zuckerberg Initiative (United States)","ror":"https://ror.org/02qenvm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210121800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joan Wong","raw_affiliation_strings":["Chan Zuckerberg Biohub, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chan Zuckerberg Biohub, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210121800"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069637310","display_name":"Vida Ahyong","orcid":"https://orcid.org/0000-0002-8632-9629"},"institutions":[{"id":"https://openalex.org/I4210121800","display_name":"Chan Zuckerberg Initiative (United States)","ror":"https://ror.org/02qenvm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210121800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vida Ahyong","raw_affiliation_strings":["Chan Zuckerberg Biohub, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chan Zuckerberg Biohub, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210121800"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062315437"],"corresponding_institution_ids":["https://openalex.org/I4210121800"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.2681,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52997558,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"25","issue":"1","first_page":"49","last_page":"49"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11934","display_name":"Syphilis Diagnosis and Treatment","score":0.37040001153945923,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11934","display_name":"Syphilis Diagnosis and Treatment","score":0.37040001153945923,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12492","display_name":"Zoonotic diseases and public health","score":0.05469999834895134,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12369","display_name":"Pneumocystis jirovecii pneumonia detection and treatment","score":0.03150000050663948,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8388628959655762},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6397953629493713},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.5435417294502258},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5357206463813782},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5274878740310669},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5270759463310242},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5252938866615295},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5221177339553833},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.49072301387786865},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.464785099029541},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44993308186531067},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.42610377073287964},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.41016918420791626}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8388628959655762},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6397953629493713},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.5435417294502258},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5357206463813782},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5274878740310669},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5270759463310242},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5252938866615295},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5221177339553833},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.49072301387786865},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.464785099029541},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44993308186531067},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.42610377073287964},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.41016918420791626},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05640-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05640-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05640-w","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:38291430","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38291430","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:pubmedcentral.nih.gov:10829301","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10829301","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10829301/pdf/12859_2024_Article_5640.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:630f1c23a7cc4de7960b92c3b230cf76","is_oa":true,"landing_page_url":"https://doaj.org/article/630f1c23a7cc4de7960b92c3b230cf76","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 25, Iss 1, Pp 1-13 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05640-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05640-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05640-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391347928.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1980388270","https://openalex.org/W2004548026","https://openalex.org/W2013410948","https://openalex.org/W2014420585","https://openalex.org/W2081555343","https://openalex.org/W2092604303","https://openalex.org/W2095599617","https://openalex.org/W2136550480","https://openalex.org/W2142428670","https://openalex.org/W2159482845","https://openalex.org/W2162057114","https://openalex.org/W2168080849","https://openalex.org/W2168917114","https://openalex.org/W2560192182","https://openalex.org/W2979864916","https://openalex.org/W3046025563","https://openalex.org/W3115825159","https://openalex.org/W4224232512","https://openalex.org/W4283777453","https://openalex.org/W4285125989","https://openalex.org/W4294216483","https://openalex.org/W4308616455","https://openalex.org/W4385519577"],"related_works":["https://openalex.org/W1961707331","https://openalex.org/W2341681417","https://openalex.org/W2063475537","https://openalex.org/W2012938657","https://openalex.org/W4223538309","https://openalex.org/W4309835295","https://openalex.org/W2096004952","https://openalex.org/W1578136679","https://openalex.org/W2087715585","https://openalex.org/W2147962989"],"abstract_inverted_index":{"BACKGROUND:":[0],"Genome":[1],"streamlining,":[2,64],"the":[3,45,60,106,124,181,189,258],"process":[4],"by":[5,27,195],"which":[6],"genomes":[7,107,119,132,229,255],"become":[8,41],"smaller":[9],"and":[10,49,67,81,120,122,136,149,152,166,220,256,271],"encode":[11],"fewer":[12],"genes":[13,48,135],"over":[14,239],"time,":[15],"is":[16,25,94,171,266],"a":[17,34,95,113,145,173,262],"common":[18],"phenomenon":[19],"among":[20],"pathogenic":[21,109,231],"bacteria.":[22,110],"This":[23],"reduction":[24],"driven":[26],"selection":[28],"for":[29,85,101,155,242,269],"minimized":[30],"energy":[31],"expenditure":[32],"in":[33,54,74,105,144,191,199,224,228,246,261],"nutrient-rich":[35],"environment.":[36],"As":[37],"pathogens":[38],"evolve":[39],"to":[40,126,157,179,211],"more":[42],"reliant":[43],"on":[44,78],"host,":[46],"metabolic":[47,68,103,160,226,244],"resulting":[50,259],"capabilities":[51],"are":[52],"lost":[53],"favor":[55],"of":[56,91,108,117,131,147,164,183,230,254],"siphoning":[57],"metabolites":[58],"from":[59],"host.":[61],"Characterizing":[62],"genome":[63,184,209,213],"gene":[65],"loss,":[66],"pathway":[69,170],"degradation":[70],"can":[71,203],"be":[72],"useful":[73],"assessing":[75],"pathogen":[76],"dependency":[77],"host":[79],"metabolism":[80],"identifying":[82,102,225,243],"potential":[83],"targets":[84],"host-directed":[86],"therapeutics.":[87],"RESULTS:":[88],"PoMeLo":[89,111,138,187,219,235,265],"(Predictor":[90],"Metabolic":[92,175],"Loss)":[93],"novel":[96],"evolutionary":[97,193],"genomics-guided":[98],"computational":[99],"approach":[100],"gaps":[104,227,245],"leverages":[112],"centralized":[114],"public":[115],"database":[116],"high-quality":[118],"annotations":[121],"allows":[123],"user":[125],"compare":[127,158],"an":[128,192,237],"unlimited":[129],"number":[130],"across":[133,251],"individual":[134,167],"pathways.":[137],"runs":[139],"locally":[140],"using":[141],"user-friendly":[142],"prompts":[143],"matter":[146],"minutes":[148],"generates":[150],"tabular":[151],"visual":[153,200],"outputs":[154],"users":[156],"predicted":[159],"capacity":[161],"between":[162],"groups":[163],"bacteria":[165],"species.":[168,233],"Each":[169],"assigned":[172],"Predicted":[174],"Loss":[176],"(PML)":[177],"score":[178],"assess":[180],"magnitude":[182],"streamlining.":[185],"Optionally,":[186],"places":[188],"results":[190],"context":[194],"including":[196],"phylogenetic":[197,263],"relationships":[198],"outputs.":[201],"It":[202],"also":[204],"initially":[205],"compute":[206],"phylogenetically-weighted":[207],"mean":[208],"sizes":[210],"identify":[212],"streamlining":[214],"events.":[215],"Here,":[216],"we":[217],"describe":[218],"demonstrate":[221],"its":[222],"use":[223,273],"Treponema":[232],"CONCLUSIONS:":[234],"represents":[236],"advance":[238],"existing":[240],"methods":[241],"genomic":[247],"data,":[248],"allowing":[249],"comparison":[250],"large":[252],"numbers":[253],"placing":[257],"data":[260],"context.":[264],"freely":[267],"available":[268],"academic":[270],"non-academic":[272],"at":[274],"https://github.com/czbiohub-sf/pomelo":[275],".":[276]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}