{"id":"https://openalex.org/W1963840676","doi":"https://doi.org/10.1371/journal.pcbi.1000761","title":"Learning \u201cgraph-mer\u201d Motifs that Predict Gene Expression Trajectories in Development","display_name":"Learning \u201cgraph-mer\u201d Motifs that Predict Gene Expression Trajectories in Development","publication_year":2010,"publication_date":"2010-04-29","ids":{"openalex":"https://openalex.org/W1963840676","doi":"https://doi.org/10.1371/journal.pcbi.1000761","mag":"1963840676","pmid":"https://pubmed.ncbi.nlm.nih.gov/20454681"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000761","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000761","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000761&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000761&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100628867","display_name":"Xuejing Li","orcid":"https://orcid.org/0000-0003-0254-141X"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xuejing Li","raw_affiliation_strings":["Department of Physics, Columbia University, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019057063","display_name":"Casandra Panea","orcid":"https://orcid.org/0000-0003-1578-2802"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Casandra Panea","raw_affiliation_strings":["Department of Genetics, Yale University, New Haven, Connecticut, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085649470","display_name":"Chris H. Wiggins","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris H. Wiggins","raw_affiliation_strings":["Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077544133","display_name":"V Reinke","orcid":"https://orcid.org/0000-0002-8967-2756"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Valerie Reinke","raw_affiliation_strings":["Department of Genetics, Yale University, New Haven, Connecticut, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085231879","display_name":"Christina S. Leslie","orcid":"https://orcid.org/0000-0002-4571-5910"},"institutions":[{"id":"https://openalex.org/I39965400","display_name":"Kettering University","ror":"https://ror.org/03rcspa57","country_code":"US","type":"education","lineage":["https://openalex.org/I39965400"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christina Leslie","raw_affiliation_strings":["Computational Biology Program, Sloan-Kettering Institute, New York, New York, United States of America"],"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Sloan-Kettering Institute, New York, New York, United States of America","institution_ids":["https://openalex.org/I39965400"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5085231879"],"corresponding_institution_ids":["https://openalex.org/I39965400"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.4066,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.61541148,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"6","issue":"4","first_page":"e1000761","last_page":"e1000761"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9970999956130981,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9970999956130981,"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":0.996399998664856,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9957000017166138,"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/biology","display_name":"Biology","score":0.6682209372520447},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6289703845977783},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5714592933654785},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5632941722869873},{"id":"https://openalex.org/keywords/caenorhabditis-elegans","display_name":"Caenorhabditis elegans","score":0.5110005140304565},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4871220588684082},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4535055160522461},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.4349018931388855},{"id":"https://openalex.org/keywords/germline","display_name":"Germline","score":0.4310370683670044},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4178019165992737}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6682209372520447},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6289703845977783},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5714592933654785},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5632941722869873},{"id":"https://openalex.org/C2778944004","wikidata":"https://www.wikidata.org/wiki/Q91703","display_name":"Caenorhabditis elegans","level":3,"score":0.5110005140304565},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4871220588684082},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4535055160522461},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.4349018931388855},{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.4310370683670044},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4178019165992737}],"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009865","descriptor_name":"Oocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009865","descriptor_name":"Oocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009865","descriptor_name":"Oocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009865","descriptor_name":"Oocytes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013094","descriptor_name":"Spermatozoa","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013094","descriptor_name":"Spermatozoa","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013094","descriptor_name":"Spermatozoa","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013094","descriptor_name":"Spermatozoa","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016018","descriptor_name":"Least-Squares Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016018","descriptor_name":"Least-Squares Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016018","descriptor_name":"Least-Squares Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016018","descriptor_name":"Least-Squares Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":10,"locations":[{"id":"doi:10.1371/journal.pcbi.1000761","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000761","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000761&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:20454681","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20454681","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:dash.harvard.edu:1/4817612","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:4817612","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"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":"","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.355.1956","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.355.1956","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/7e/a6/PLoS_Comput_Biol_2010_Apr_29_6(4)_e1000761.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000761","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000761","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:academiccommons.columbia.edu:10.7916/D8B56H8X","is_oa":false,"landing_page_url":"https://doi.org/10.7916/D8B56H8X","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Articles"},{"id":"pmh:oai:doaj.org/article:8f9b13f146d9491184cfa67bc4c4e84c","is_oa":true,"landing_page_url":"https://doaj.org/article/8f9b13f146d9491184cfa67bc4c4e84c","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 6, Iss 4, p e1000761 (2010)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/143690","is_oa":true,"landing_page_url":"https://figshare.com/articles/Learning_graph_mer_Motifs_that_Predict_Gene_Expression_Trajectories_in_Development/143690","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2861633","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2861633","pdf_url":null,"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":"PLoS Comput Biol","raw_type":"Text"},{"id":"doi:10.7916/d8b56h8x","is_oa":true,"landing_page_url":"https://doi.org/10.7916/d8b56h8x","pdf_url":null,"source":{"id":"https://openalex.org/S4306402601","display_name":"Columbia Academic Commons (Columbia University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78577930","host_organization_name":"Columbia University","host_organization_lineage":["https://openalex.org/I78577930"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000761","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000761","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000761&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5899999737739563,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G113550954","display_name":"III-CXT: Learning from graph-structured data: new algorithms for modeling physical interactions in cellular networks","funder_award_id":"0705580","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2214386018","display_name":null,"funder_award_id":"U54-CA121852","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G297152156","display_name":null,"funder_award_id":"CA121852","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308571","display_name":"North Carolina Biotechnology Center","ror":"https://ror.org/03hj4jr80"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1963840676.pdf","grobid_xml":"https://content.openalex.org/works/W1963840676.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1578099820","https://openalex.org/W1592870802","https://openalex.org/W1650502025","https://openalex.org/W1906461790","https://openalex.org/W1969307568","https://openalex.org/W1976251851","https://openalex.org/W1980253661","https://openalex.org/W1982445747","https://openalex.org/W2009001778","https://openalex.org/W2039896429","https://openalex.org/W2051139824","https://openalex.org/W2054578424","https://openalex.org/W2063473501","https://openalex.org/W2073727170","https://openalex.org/W2090093846","https://openalex.org/W2097057782","https://openalex.org/W2100648873","https://openalex.org/W2101883862","https://openalex.org/W2104290444","https://openalex.org/W2104780023","https://openalex.org/W2119862467","https://openalex.org/W2129265801","https://openalex.org/W2135046866","https://openalex.org/W2136850043","https://openalex.org/W2138049103","https://openalex.org/W2141408320","https://openalex.org/W2144710927","https://openalex.org/W2148470786","https://openalex.org/W2151464048","https://openalex.org/W2155103279","https://openalex.org/W2159675211","https://openalex.org/W2162491638","https://openalex.org/W2165874743","https://openalex.org/W2167190345","https://openalex.org/W2285103646","https://openalex.org/W2572321817","https://openalex.org/W2997701990","https://openalex.org/W4390473083","https://openalex.org/W6684578312"],"related_works":["https://openalex.org/W2230364071","https://openalex.org/W2073515060","https://openalex.org/W2142881677","https://openalex.org/W2277277196","https://openalex.org/W2043274041","https://openalex.org/W4390649590","https://openalex.org/W2157076973","https://openalex.org/W1570050666","https://openalex.org/W1976817370","https://openalex.org/W1927891221"],"abstract_inverted_index":{"A":[0,28],"key":[1],"problem":[2,34],"in":[3,16,48,54,76,84,101,132,173,239],"understanding":[4],"transcriptional":[5],"regulatory":[6,12,68,125,229],"networks":[7],"is":[8,14],"deciphering":[9],"what":[10],"cis":[11,124],"logic":[13],"encoded":[15],"gene":[17,73,129,163,241],"promoter":[18,50,118],"sequences":[19,51],"and":[20,42,127,181,192,200,238,256],"how":[21],"this":[22,33],"sequence":[23,119,154],"information":[24],"maps":[25],"to":[26,32,97,120,122,152,169,187,207,216],"expression.":[27,242],"typical":[29],"computational":[30],"approach":[31,168],"involves":[35],"clustering":[36],"genes":[37,53,58],"by":[38,66,156],"their":[39],"expression":[40,61,74,130,164,188,266],"profiles":[41,62,75,189],"then":[43],"searching":[44],"for":[45,110,190],"overrepresented":[46],"motifs":[47,126,202,214,260],"the":[49,85,102,112,167,179,204,223],"of":[52,87,115,146,158,226,233],"a":[55,77,107,138,143],"cluster.":[56],"However,":[57],"with":[59],"similar":[60],"may":[63,94],"be":[64,95],"controlled":[65],"distinct":[67],"programs.":[69],"Moreover,":[70],"if":[71],"many":[72],"data":[78],"set":[79],"are":[80],"highly":[81],"correlated,":[82],"as":[83],"case":[86],"whole":[88],"organism":[89],"developmental":[90,133,263],"time":[91,134,264],"series,":[92],"it":[93],"difficult":[96],"resolve":[98],"fine-grained":[99],"clusters":[100],"first":[103,180],"place.":[104],"We":[105,136,196,219],"present":[106],"predictive":[108],"framework":[109],"modeling":[111],"natural":[113],"flow":[114],"information,":[116],"from":[117,203,261],"expression,":[121],"learn":[123,153,251],"characterize":[128],"patterns":[131],"courses.":[135],"introduce":[137],"cluster-free":[139],"algorithm":[140],"based":[141],"on":[142],"graph-regularized":[144],"version":[145],"partial":[147],"least":[148],"squares":[149],"(PLS)":[150],"regression":[151,248],"patterns--represented":[155],"graphs":[157],"k-mers,":[159],"or":[160],"\"graph-mers\"--that":[161],"predict":[162],"trajectories.":[165],"Applying":[166],"wildtype":[170],"germline":[171],"development":[172],"Caenorhabditis":[174],"elegans,":[175],"we":[176],"found":[177,220],"that":[178,246],"second":[182],"latent":[183,254],"PLS":[184],"factors":[185],"mapped":[186],"oocyte":[191,217],"sperm":[193],"genes,":[194],"respectively.":[195],"extracted":[197],"both":[198],"known":[199],"novel":[201,212],"graph-mers":[205],"associated":[206],"these":[208,227],"germline-specific":[209],"patterns,":[210],"including":[211],"CG-rich":[213],"specific":[215],"genes.":[218],"evidence":[221],"supporting":[222],"functional":[224,259],"relevance":[225],"putative":[228],"elements":[230],"through":[231],"analysis":[232],"positional":[234],"bias,":[235],"motif":[236],"conservation":[237],"situ":[240],"This":[243],"study":[244],"demonstrates":[245],"our":[247],"model":[249],"can":[250],"biologically":[252],"meaningful":[253],"structure":[255],"identify":[257],"potentially":[258],"subtle":[262],"course":[265],"data.":[267]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
