{"id":"https://openalex.org/W4400344187","doi":"https://doi.org/10.1093/bioinformatics/btae363","title":"Pangenome graph layout by Path-Guided Stochastic Gradient Descent","display_name":"Pangenome graph layout by Path-Guided Stochastic Gradient Descent","publication_year":2024,"publication_date":"2024-07-01","ids":{"openalex":"https://openalex.org/W4400344187","doi":"https://doi.org/10.1093/bioinformatics/btae363","pmid":"https://pubmed.ncbi.nlm.nih.gov/38960860"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/7/btae363/58463786/btae363.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/article-pdf/40/7/btae363/58463786/btae363.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040033163","display_name":"Simon Heumos","orcid":"https://orcid.org/0000-0003-3326-817X"},"institutions":[{"id":"https://openalex.org/I4210125796","display_name":"University Children's Hospital T\u00fcbingen","ror":"https://ror.org/03esvmb28","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094118","https://openalex.org/I4210125796"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Simon Heumos","raw_affiliation_strings":["Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","Institute for Bioinformatics and Medical Informatics (IBMI), University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","M3 Research Center, University Hospital T\u00fcbingen , 72076 T\u00fcbingen, Germany","Quantitative Biology Center (QBiC), University of T\u00fcbingen , 72076 T\u00fcbingen, Germany"],"affiliations":[{"raw_affiliation_string":"Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Institute for Bioinformatics and Medical Informatics (IBMI), University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"M3 Research Center, University Hospital T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210125796"]},{"raw_affiliation_string":"Quantitative Biology Center (QBiC), University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028113588","display_name":"Andrea Guarracino","orcid":"https://orcid.org/0000-0001-9744-131X"},"institutions":[{"id":"https://openalex.org/I160606119","display_name":"University of Tennessee Health Science Center","ror":"https://ror.org/0011qv509","country_code":"US","type":"education","lineage":["https://openalex.org/I160606119"]},{"id":"https://openalex.org/I4210115812","display_name":"Human Technopole","ror":"https://ror.org/029gmnc79","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210115812"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Andrea Guarracino","raw_affiliation_strings":["Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, United States","Genomics Research Centre, Human Technopole , 20157 Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, United States","institution_ids":["https://openalex.org/I160606119"]},{"raw_affiliation_string":"Genomics Research Centre, Human Technopole , 20157 Milan, Italy","institution_ids":["https://openalex.org/I4210115812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5098488960","display_name":"Jan-Niklas Schmelzle","orcid":"https://orcid.org/0000-0001-8566-4049"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Jan-Niklas M Schmelzle","raw_affiliation_strings":["Department of Computer Engineering, School of Computation, Information and Technology (CIT), Technical University of Munich , 80333 Munich, Germany","School of Electrical and Computer Engineering, Cornell University , Ithaca, NY 14853, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, School of Computation, Information and Technology (CIT), Technical University of Munich , 80333 Munich, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"School of Electrical and Computer Engineering, Cornell University , Ithaca, NY 14853, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074049091","display_name":"Jiajie Li","orcid":"https://orcid.org/0000-0002-6775-2843"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiajie Li","raw_affiliation_strings":["School of Electrical and Computer Engineering, Cornell University , Ithaca, NY 14853, United States"],"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Cornell University , Ithaca, NY 14853, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037210004","display_name":"Zhiru Zhang","orcid":"https://orcid.org/0000-0002-0778-0308"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhiru Zhang","raw_affiliation_strings":["School of Electrical and Computer Engineering, Cornell University , Ithaca, NY 14853, United States"],"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Cornell University , Ithaca, NY 14853, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064601625","display_name":"J\u00f6rg Hagmann","orcid":"https://orcid.org/0000-0002-7232-3103"},"institutions":[{"id":"https://openalex.org/I4210133934","display_name":"Bernstein Center for Computational Neuroscience T\u00fcbingen","ror":"https://ror.org/03kfnwp54","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210092532","https://openalex.org/I4210133934"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"J\u00f6rg Hagmann","raw_affiliation_strings":["Computomics GmbH , 72072 T\u00fcbingen, Germany"],"affiliations":[{"raw_affiliation_string":"Computomics GmbH , 72072 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210133934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008496386","display_name":"Sven Nahnsen","orcid":"https://orcid.org/0000-0002-4375-0691"},"institutions":[{"id":"https://openalex.org/I4210125796","display_name":"University Children's Hospital T\u00fcbingen","ror":"https://ror.org/03esvmb28","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094118","https://openalex.org/I4210125796"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sven Nahnsen","raw_affiliation_strings":["Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","Institute for Bioinformatics and Medical Informatics (IBMI), University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","M3 Research Center, University Hospital T\u00fcbingen , 72076 T\u00fcbingen, Germany","Quantitative Biology Center (QBiC), University of T\u00fcbingen , 72076 T\u00fcbingen, Germany"],"affiliations":[{"raw_affiliation_string":"Biomedical Data Science, Department of Computer Science, University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Institute for Bioinformatics and Medical Informatics (IBMI), University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"M3 Research Center, University Hospital T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210125796"]},{"raw_affiliation_string":"Quantitative Biology Center (QBiC), University of T\u00fcbingen , 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028085028","display_name":"Pjotr Prins","orcid":"https://orcid.org/0000-0002-8021-9162"},"institutions":[{"id":"https://openalex.org/I160606119","display_name":"University of Tennessee Health Science Center","ror":"https://ror.org/0011qv509","country_code":"US","type":"education","lineage":["https://openalex.org/I160606119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pjotr Prins","raw_affiliation_strings":["Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, United States"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, United States","institution_ids":["https://openalex.org/I160606119"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008992371","display_name":"Erik Garrison","orcid":"https://orcid.org/0000-0003-3821-631X"},"institutions":[{"id":"https://openalex.org/I160606119","display_name":"University of Tennessee Health Science Center","ror":"https://ror.org/0011qv509","country_code":"US","type":"education","lineage":["https://openalex.org/I160606119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik Garrison","raw_affiliation_strings":["Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, United States"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, United States","institution_ids":["https://openalex.org/I160606119"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5040033163"],"corresponding_institution_ids":["https://openalex.org/I4210125796","https://openalex.org/I8087733"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6028,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.82986489,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"40","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9969000220298767,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9969000220298767,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9961000084877014,"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":0.9948999881744385,"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/graph","display_name":"Graph","score":0.6314482688903809},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5413723587989807},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5299699306488037},{"id":"https://openalex.org/keywords/graph-drawing","display_name":"Graph drawing","score":0.49906015396118164},{"id":"https://openalex.org/keywords/graph-layout","display_name":"Graph Layout","score":0.4469708502292633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40677040815353394},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3913848400115967},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36254483461380005},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.1518324315547943},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14459958672523499}],"concepts":[{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6314482688903809},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5413723587989807},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5299699306488037},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.49906015396118164},{"id":"https://openalex.org/C2911174283","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph Layout","level":4,"score":0.4469708502292633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40677040815353394},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3913848400115967},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36254483461380005},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.1518324315547943},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14459958672523499}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"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":"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":"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":"D016678","descriptor_name":"Genome","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/7/btae363/58463786/btae363.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:38960860","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38960860","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:pubmedcentral.nih.gov:11227364","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11227364","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11227364/pdf/btae363.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae363","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae363","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/7/btae363/58463786/btae363.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":[],"awards":[{"id":"https://openalex.org/G1147967356","display_name":null,"funder_award_id":"031A533A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G1159569226","display_name":null,"funder_award_id":"031A534A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G1254183670","display_name":null,"funder_award_id":"031A538A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G1511448630","display_name":null,"funder_award_id":"031A537D","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G1741599539","display_name":null,"funder_award_id":"031A537C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2414046978","display_name":null,"funder_award_id":"031A533A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2768250103","display_name":null,"funder_award_id":"031A537A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G3263214147","display_name":null,"funder_award_id":"U01DA047638","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4480115467","display_name":null,"funder_award_id":"031A535A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4780366467","display_name":null,"funder_award_id":"31A535A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5088104505","display_name":null,"funder_award_id":"de.NBI","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5128364324","display_name":null,"funder_award_id":"31A532B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5150729208","display_name":null,"funder_award_id":"R01GM123489","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5157400669","display_name":null,"funder_award_id":"031A537A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5828315659","display_name":null,"funder_award_id":"031A538A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5870080920","display_name":null,"funder_award_id":"031A537D","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5940054534","display_name":null,"funder_award_id":"de.NBI Cloud","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6137013498","display_name":null,"funder_award_id":"2180-390900677","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6303721240","display_name":null,"funder_award_id":"031A535A","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G6418569106","display_name":null,"funder_award_id":"031A532B","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G6557565170","display_name":null,"funder_award_id":"031A537B","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G6955755495","display_name":null,"funder_award_id":"Germany","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7086918339","display_name":null,"funder_award_id":"031A534A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7564846446","display_name":null,"funder_award_id":"2118709","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8126315642","display_name":null,"funder_award_id":"031A532B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8377217958","display_name":null,"funder_award_id":"031A533B","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"},{"id":"https://openalex.org/G8387372653","display_name":null,"funder_award_id":"031A533B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8452288796","display_name":null,"funder_award_id":"031A537B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"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/G8628892960","display_name":null,"funder_award_id":"GM123489","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8739132553","display_name":null,"funder_award_id":"031A533","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8953674659","display_name":null,"funder_award_id":"031A537C","funder_id":"https://openalex.org/F4320330124","funder_display_name":"German Network for Bioinformatics Infrastructure"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320323803","display_name":"Bundesministerium f\u00fcr Wirtschaft und Energie","ror":"https://ror.org/02vgg2808"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400344187.pdf","grobid_xml":"https://content.openalex.org/works/W4400344187.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W2037959956","https://openalex.org/W2093610003","https://openalex.org/W2115111616","https://openalex.org/W2254458779","https://openalex.org/W2547528004","https://openalex.org/W2604272474","https://openalex.org/W2797920702","https://openalex.org/W2888300707","https://openalex.org/W2952366981","https://openalex.org/W2953263404","https://openalex.org/W2966929769","https://openalex.org/W3005228641","https://openalex.org/W4220999759","https://openalex.org/W4255836900","https://openalex.org/W4280583823","https://openalex.org/W4289388808","https://openalex.org/W4308878077","https://openalex.org/W4316507600","https://openalex.org/W4376132855","https://openalex.org/W4376133202","https://openalex.org/W4389010703","https://openalex.org/W6691736922","https://openalex.org/W6757799534","https://openalex.org/W6795410112","https://openalex.org/W6849005662"],"related_works":["https://openalex.org/W2346931493","https://openalex.org/W2031908202","https://openalex.org/W2766563406","https://openalex.org/W3160329999","https://openalex.org/W2026729066","https://openalex.org/W2903996962","https://openalex.org/W2895526338","https://openalex.org/W4312076339","https://openalex.org/W1555430809","https://openalex.org/W1593721195"],"abstract_inverted_index":{"We":[0],"integrated":[1],"PG-SGD":[2],"in":[3],"ODGI":[4],"which":[5],"is":[6,19],"released":[7],"as":[8],"free":[9],"software":[10],"under":[11],"the":[12],"MIT":[13],"open":[14],"source":[15],"license.":[16],"Source":[17],"code":[18],"available":[20],"at":[21],"https://github.com/pangenome/odgi.":[22]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
