{"id":"https://openalex.org/W194469646","doi":"https://doi.org/10.1007/978-1-60327-159-2_10","title":"Reconstruction of Full-Length Isoforms from Splice Graphs","display_name":"Reconstruction of Full-Length Isoforms from Splice Graphs","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W194469646","doi":"https://doi.org/10.1007/978-1-60327-159-2_10","mag":"194469646","pmid":"https://pubmed.ncbi.nlm.nih.gov/18566766"},"language":"en","primary_location":{"id":"doi:10.1007/978-1-60327-159-2_10","doi":"https://doi.org/10.1007/978-1-60327-159-2_10","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-60327-159-2_10","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology\u2122","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W2412318916","display_name":"Bioinformatics"},"type":"book-chapter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087568641","display_name":"Yi Xing","orcid":"https://orcid.org/0000-0001-9257-7613","observed_orcids":["https://orcid.org/0000-0001-9257-7613"]},"institutions":[{"id":"https://openalex.org/I126307644","display_name":"University of Iowa","ror":"https://ror.org/036jqmy94","country_code":"US","type":"education","lineage":["https://openalex.org/I126307644"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Xing","raw_affiliation_strings":["Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA","Department of Internal Medicine, Carver College of Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA","institution_ids":["https://openalex.org/I126307644"]},{"raw_affiliation_string":"Department of Internal Medicine, Carver College of Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA","institution_ids":["https://openalex.org/I126307644"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103393374","display_name":"Christopher J. Lee","orcid":"https://orcid.org/0000-0001-8360-8756","observed_orcids":["https://orcid.org/0000-0001-8360-8756"]},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Lee","raw_affiliation_strings":["Molecular Biology Institute, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Biology Institute, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.2779,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.78998797,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"452","issue":null,"first_page":"199","last_page":"205"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9092000126838684,"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/T10604","display_name":"RNA Research and Splicing","score":0.9092000126838684,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.08169999718666077,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0010000000474974513,"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/alternative-splicing","display_name":"alternative splicing","score":0.9010000228881836},{"id":"https://openalex.org/keywords/pre-mrna-splicing","display_name":"pre-mRNA splicing","score":0.8510000109672546},{"id":"https://openalex.org/keywords/expressed-sequence-tags","display_name":"expressed sequence tags","score":0.7689999938011169},{"id":"https://openalex.org/keywords/oligonucleotide-microarrays","display_name":"oligonucleotide microarrays","score":0.9369999766349792}],"concepts":[{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.6778829097747803},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.6302660703659058},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6140846014022827},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.6000823974609375},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.5966684222221375},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5108804106712341},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.498960018157959},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4431169927120209},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4255830943584442},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.41967886686325073},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3931567966938019},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29905223846435547},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2605092525482178},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2297128438949585},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10608914494514465},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07846090197563171}],"mesh":[{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012322","descriptor_name":"RNA Precursors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1007/978-1-60327-159-2_10","doi":"https://doi.org/10.1007/978-1-60327-159-2_10","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-60327-159-2_10","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology\u2122","raw_type":"book-chapter"},{"id":"pmid:18566766","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18566766","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,"listed_in":[],"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":"Methods in molecular biology (Clifton, N.J.)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5071496643","display_name":"Center for Computational Biology (CCB)(RMI)","funder_award_id":"U54RR021813","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1797365312","https://openalex.org/W1967618835","https://openalex.org/W2001952613","https://openalex.org/W2024039709","https://openalex.org/W2077199821","https://openalex.org/W2113267877","https://openalex.org/W2113322429","https://openalex.org/W2115160938","https://openalex.org/W2128001071","https://openalex.org/W2143345980","https://openalex.org/W2143447881","https://openalex.org/W2151450179","https://openalex.org/W2153242254","https://openalex.org/W2154954867","https://openalex.org/W2158679652","https://openalex.org/W7096691620","https://openalex.org/W7101005564"],"related_works":["https://openalex.org/W2952424604","https://openalex.org/W2154954867","https://openalex.org/W2156952275","https://openalex.org/W7095975274","https://openalex.org/W2101199515","https://openalex.org/W7096691620","https://openalex.org/W2025119259","https://openalex.org/W3157702769","https://openalex.org/W2794114531","https://openalex.org/W2905139251"],"abstract_inverted_index":{"Most":[0],"alternative":[1,47],"splicing":[2],"events":[3],"in":[4],"human":[5],"and":[6,25,40],"other":[7],"eukaryotic":[8],"genomes":[9],"are":[10],"detected":[11],"using":[12],"sequence":[13,34],"fragments":[14,35],"produced":[15],"by":[16],"high":[17],"throughput":[18],"genomic":[19],"technologies,":[20],"such":[21,33],"as":[22],"EST":[23],"sequencing":[24],"oligonucleotide":[26],"microarrays.":[27],"Reconstructing":[28],"full-length":[29,60],"transcript":[30],"isoforms":[31],"from":[32],"is":[36],"a":[37,52],"major":[38],"interest":[39],"challenge":[41],"for":[42,56],"computational":[43,57],"analyses":[44],"of":[45,59],"pre-mRNA":[46],"splicing.":[48],"This":[49],"chapter":[50],"describes":[51],"general":[53],"graph-based":[54],"approach":[55],"inference":[58],"isoforms.":[61]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}