{"id":"https://openalex.org/W2042132281","doi":"https://doi.org/10.1186/1471-2105-15-122","title":"Transcript mapping based on dRNA-seq data","display_name":"Transcript mapping based on dRNA-seq data","publication_year":2014,"publication_date":"2014-04-29","ids":{"openalex":"https://openalex.org/W2042132281","doi":"https://doi.org/10.1186/1471-2105-15-122","mag":"2042132281","pmid":"https://pubmed.ncbi.nlm.nih.gov/24780064"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-122","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-122","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-122","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-122","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040688806","display_name":"Thorsten Bischler","orcid":"https://orcid.org/0000-0001-9288-9481"},"institutions":[{"id":"https://openalex.org/I25974101","display_name":"University of W\u00fcrzburg","ror":"https://ror.org/00fbnyb24","country_code":"DE","type":"education","lineage":["https://openalex.org/I25974101"]},{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Thorsten Bischler","raw_affiliation_strings":["Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Sch\u00e4nzlestr. 1, 79104, Freiburg, Germany","Institute for Molecular Infection Biology, Julius-Maximilians-University W\u00fcrzburg, Josef-Schneider-Str. 2/D15, 97080, W\u00fcrzburg, Germany","Institute for Molecular Infection Biology, Julius-Maximilians-University W\u00fcrzburg, W\u00fcrzburg, Germany","Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Sch\u00e4nzlestr. 1, 79104, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Institute for Molecular Infection Biology, Julius-Maximilians-University W\u00fcrzburg, Josef-Schneider-Str. 2/D15, 97080, W\u00fcrzburg, Germany","institution_ids":["https://openalex.org/I25974101"]},{"raw_affiliation_string":"Institute for Molecular Infection Biology, Julius-Maximilians-University W\u00fcrzburg, W\u00fcrzburg, Germany","institution_ids":[]},{"raw_affiliation_string":"Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068109215","display_name":"Matthias Kopf","orcid":null},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias Kopf","raw_affiliation_strings":["Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Sch\u00e4nzlestr. 1, 79104, Freiburg, Germany","Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Sch\u00e4nzlestr. 1, 79104, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044044433","display_name":"Bj\u00f6rn Vo\u00df","orcid":"https://orcid.org/0000-0002-5377-2800"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bj\u00f6rn Vo\u00df","raw_affiliation_strings":["Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Sch\u00e4nzlestr, 1, 79104 Freiburg, Germany. bjoern.voss@biologie.uni-freiburg.de","Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Sch\u00e4nzlestr, 1, 79104 Freiburg, Germany. bjoern.voss@biologie.uni-freiburg.de","institution_ids":[]},{"raw_affiliation_string":"Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5040688806"],"corresponding_institution_ids":["https://openalex.org/I161046081","https://openalex.org/I25974101"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1447,"currency":"EUR","value_usd":1560},"fwci":1.2834,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.79151764,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"122","last_page":"122"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9940999746322632,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9854000210762024,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/rna-seq","display_name":"RNA-Seq","score":0.6705212593078613},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5894345641136169},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4787939488887787},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45226800441741943},{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.43103331327438354},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.41382575035095215},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37391334772109985},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32647544145584106},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23575624823570251},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20646372437477112},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13001364469528198}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6705212593078613},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5894345641136169},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4787939488887787},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45226800441741943},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.43103331327438354},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41382575035095215},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37391334772109985},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32647544145584106},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23575624823570251},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20646372437477112},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13001364469528198},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0}],"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":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-15-122","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-122","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-122","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24780064","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24780064","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3005930","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4016656","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:freidok.uni-freiburg.de:12490","is_oa":false,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bsz:25-freidok-124901","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC bioinformatics. 15 (2014), 122, DOI 10.1186/1471-2105-15-122, issn: 1471-2105","raw_type":"article"},{"id":"pmh:oai:opus.bibliothek.uni-wuerzburg.de:11666","is_oa":true,"landing_page_url":"https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-116663","pdf_url":null,"source":{"id":"https://openalex.org/S4306401635","display_name":"Online Publication Service of W\u00fcrzburg University (W\u00fcrzburg University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I25974101","host_organization_name":"University of W\u00fcrzburg","host_organization_lineage":["https://openalex.org/I25974101"],"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":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-122","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-122","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-122","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7300000190734863,"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8"}],"awards":[{"id":"https://openalex.org/G4704746504","display_name":null,"funder_award_id":"Vo 1450/2-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6052429835","display_name":null,"funder_award_id":"(DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2042132281.pdf","grobid_xml":"https://content.openalex.org/works/W2042132281.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1969225831","https://openalex.org/W1981509058","https://openalex.org/W1990937720","https://openalex.org/W2000875411","https://openalex.org/W2005436483","https://openalex.org/W2015658598","https://openalex.org/W2016170819","https://openalex.org/W2054522148","https://openalex.org/W2062896692","https://openalex.org/W2097341408","https://openalex.org/W2098832713","https://openalex.org/W2112491476","https://openalex.org/W2138873633","https://openalex.org/W2140022443","https://openalex.org/W2141458291","https://openalex.org/W2166406784","https://openalex.org/W2170488656"],"related_works":["https://openalex.org/W4362511917","https://openalex.org/W2904597490","https://openalex.org/W4362530199","https://openalex.org/W4362511560","https://openalex.org/W4377231761","https://openalex.org/W4285162488","https://openalex.org/W4362512073","https://openalex.org/W4362485908","https://openalex.org/W2268123450","https://openalex.org/W2093288248"],"abstract_inverted_index":{"With":[0],"our":[1],"algorithm":[2],"it":[3],"is":[4],"possible":[5],"to":[6],"identify":[7],"operons":[8],"and":[9,11,26],"5'-":[10],"3'-UTRs":[12],"in":[13,30],"an":[14],"automated":[15],"fashion.":[16],"This":[17],"alleviates":[18],"the":[19,31],"need":[20],"for":[21],"labour":[22],"intensive":[23],"manual":[24],"inspection":[25],"enables":[27],"large-scale":[28],"studies":[29],"area":[32],"of":[33],"comparative":[34],"transcriptomics.":[35]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}