{"id":"https://openalex.org/W4399694788","doi":"https://doi.org/10.1093/bioinformatics/btae361","title":"Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach","display_name":"Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399694788","doi":"https://doi.org/10.1093/bioinformatics/btae361","pmid":"https://pubmed.ncbi.nlm.nih.gov/38870525"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae361","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae361/58238097/btae361.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae361/58238097/btae361.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030824535","display_name":"Yueyu Jiang","orcid":"https://orcid.org/0000-0001-8425-7556"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yueyu Jiang","raw_affiliation_strings":["Electrical and Computer Engineering Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","Electrical and Computer Engineering Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States"],"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Electrical and Computer Engineering Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022461817","display_name":"Daniel McDonald","orcid":"https://orcid.org/0000-0003-0876-9060"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel McDonald","raw_affiliation_strings":["Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States"],"affiliations":[{"raw_affiliation_string":"Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036045086","display_name":"Daniela S. Perry","orcid":"https://orcid.org/0000-0001-6870-1194"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniela Perry","raw_affiliation_strings":["Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States"],"affiliations":[{"raw_affiliation_string":"Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033881627","display_name":"Rob Knight","orcid":"https://orcid.org/0000-0002-0975-9019"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Knight","raw_affiliation_strings":["Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States"],"affiliations":[{"raw_affiliation_string":"Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Pediatrics Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087959579","display_name":"Siavash Mirarab","orcid":"https://orcid.org/0000-0001-5410-1518"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siavash Mirarab","raw_affiliation_strings":["Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","Electrical and Computer Engineering Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","Electrical and Computer Engineering Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States"],"affiliations":[{"raw_affiliation_string":"Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Electrical and Computer Engineering Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Electrical and Computer Engineering Department, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego , 9500 Gilman Dr , La Jolla, CA, 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5030824535"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4579,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.63061614,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"40","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9918000102043152,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9897000193595886,"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":0.7194015383720398},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6843211054801941},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6255114078521729},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6077338457107544},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5990472435951233},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5480029582977295},{"id":"https://openalex.org/keywords/divide-and-conquer-algorithms","display_name":"Divide and conquer algorithms","score":0.506077229976654},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4629974961280823},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42146530747413635},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34491950273513794},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33081525564193726},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2514990568161011},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2333659827709198},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16087982058525085},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14770972728729248},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09947791695594788}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7194015383720398},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6843211054801941},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6255114078521729},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6077338457107544},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5990472435951233},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5480029582977295},{"id":"https://openalex.org/C71559656","wikidata":"https://www.wikidata.org/wiki/Q671298","display_name":"Divide and conquer algorithms","level":2,"score":0.506077229976654},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4629974961280823},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42146530747413635},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34491950273513794},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33081525564193726},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2514990568161011},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2333659827709198},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16087982058525085},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14770972728729248},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09947791695594788},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btae361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae361","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae361/58238097/btae361.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38870525","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38870525","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7mv169jp","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7mv169jp","pdf_url":"https://escholarship.org/content/qt7mv169jp/qt7mv169jp.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 40, iss 6","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11193062","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11193062","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11193062/pdf/btae361.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:ark:/13030/qt7mv169jp","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae361","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae361/58238097/btae361.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G1450486485","display_name":null,"funder_award_id":"150046","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1912064254","display_name":null,"funder_award_id":"2137603","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2507572247","display_name":null,"funder_award_id":"2138286","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G34258105","display_name":null,"funder_award_id":"2138307","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4006316252","display_name":null,"funder_award_id":"2138259","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4010157413","display_name":null,"funder_award_id":"2138259","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G4275568664","display_name":null,"funder_award_id":"2138286","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4676224565","display_name":null,"funder_award_id":"2138296","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4801515358","display_name":null,"funder_award_id":"ACCESS","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G509285653","display_name":null,"funder_award_id":"2138307","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5156331529","display_name":null,"funder_award_id":"2138296","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5464919783","display_name":null,"funder_award_id":"2137603","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G5661333668","display_name":null,"funder_award_id":"R35GM142725","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5665456810","display_name":null,"funder_award_id":"2100237","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6664589177","display_name":null,"funder_award_id":"2138307","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G7526614437","display_name":null,"funder_award_id":"2137603","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7622549653","display_name":null,"funder_award_id":"213829","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8300691027","display_name":null,"funder_award_id":"2138286","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8499740153","display_name":null,"funder_award_id":"2138259","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8897435675","display_name":null,"funder_award_id":"2138296","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320316545","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337377","display_name":"Office of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4399694788.pdf"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1748508858","https://openalex.org/W1822648038","https://openalex.org/W1988925586","https://openalex.org/W2033900229","https://openalex.org/W2034285706","https://openalex.org/W2045449780","https://openalex.org/W2060425093","https://openalex.org/W2125230147","https://openalex.org/W2126325593","https://openalex.org/W2139478957","https://openalex.org/W2141052558","https://openalex.org/W2145562754","https://openalex.org/W2147461064","https://openalex.org/W2150815933","https://openalex.org/W2150884987","https://openalex.org/W2161973008","https://openalex.org/W2593591803","https://openalex.org/W2603078022","https://openalex.org/W2800461749","https://openalex.org/W2811244727","https://openalex.org/W2889019390","https://openalex.org/W2892206041","https://openalex.org/W2897603717","https://openalex.org/W2904155504","https://openalex.org/W2908692794","https://openalex.org/W2913309890","https://openalex.org/W2949867654","https://openalex.org/W2951358594","https://openalex.org/W2951540755","https://openalex.org/W2969491951","https://openalex.org/W2975848703","https://openalex.org/W2990925943","https://openalex.org/W2991998196","https://openalex.org/W3028280407","https://openalex.org/W3160568774","https://openalex.org/W3205793393","https://openalex.org/W4206573133","https://openalex.org/W4225003079","https://openalex.org/W4226048102","https://openalex.org/W4226049731","https://openalex.org/W4291415207","https://openalex.org/W4293008343","https://openalex.org/W4302763624","https://openalex.org/W4306851531","https://openalex.org/W4313451807","https://openalex.org/W4385331223","https://openalex.org/W6658825153","https://openalex.org/W6842448306"],"related_works":["https://openalex.org/W2352794675","https://openalex.org/W1539994214","https://openalex.org/W2111712077","https://openalex.org/W2051228988","https://openalex.org/W4247094814","https://openalex.org/W108531593","https://openalex.org/W2487162673","https://openalex.org/W2114617541","https://openalex.org/W2894446834","https://openalex.org/W2113265763"],"abstract_inverted_index":{"The":[0],"dataset":[1],"and":[2],"C-DEPP":[3],"software":[4],"are":[5],"freely":[6],"available":[7],"at":[8],"https://github.com/yueyujiang/dataset_cdepp/.":[9]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}