{"id":"https://openalex.org/W2136090938","doi":"https://doi.org/10.1093/bioinformatics/bts189","title":"TSSi\u2014an R package for transcription start site identification from 5\u2032 mRNA tag data","display_name":"TSSi\u2014an R package for transcription start site identification from 5\u2032 mRNA tag data","publication_year":2012,"publication_date":"2012-04-17","ids":{"openalex":"https://openalex.org/W2136090938","doi":"https://doi.org/10.1093/bioinformatics/bts189","mag":"2136090938","pmid":"https://pubmed.ncbi.nlm.nih.gov/22513994"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts189","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1641/48872190/bioinformatics_28_12_1641.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1641/48872190/bioinformatics_28_12_1641.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076933919","display_name":"Clemens Kreutz","orcid":"https://orcid.org/0000-0002-8796-5766"},"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":true,"raw_author_name":"C. Kreutz","raw_affiliation_strings":["1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077047807","display_name":"Julian Gehring","orcid":"https://orcid.org/0000-0003-0070-4975"},"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":"J. S. Gehring","raw_affiliation_strings":["1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036441626","display_name":"Daniel Lang","orcid":"https://orcid.org/0000-0002-2166-0716"},"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":"D. Lang","raw_affiliation_strings":["1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002023600","display_name":"Ralf Reski","orcid":"https://orcid.org/0000-0002-5496-6711"},"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":"R. Reski","raw_affiliation_strings":["1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052831097","display_name":"Jens Timmer","orcid":"https://orcid.org/0000-0003-4517-1383"},"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":"J. Timmer","raw_affiliation_strings":["1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047370853","display_name":"Stefan A. Rensing","orcid":"https://orcid.org/0000-0002-0225-873X"},"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":"S. A. Rensing","raw_affiliation_strings":["1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"1 Institute for Physics, University of Freiburg, Germany, 2Freiburg Center for Systems Biology (ZBSA), University of Freiburg, Germany, 3Faculty of Biology, University of Freiburg, Germany, 4Freiburg Initiative in Systems Biology (FRISYS), University of Freiburg, Germany, 5Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Germany and 6BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5076933919"],"corresponding_institution_ids":["https://openalex.org/I161046081"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2627,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.58208596,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"28","issue":"12","first_page":"1641","last_page":"1642"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.998199999332428,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.998199999332428,"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/T10604","display_name":"RNA Research and Splicing","score":0.998199999332428,"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":0.9968000054359436,"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/identification","display_name":"Identification (biology)","score":0.6528669595718384},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5692840218544006},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5210391879081726},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.5097629427909851},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5053656697273254},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5012476444244385},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.42397454380989075},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3565092086791992},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2887153625488281},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2634925842285156},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15114876627922058},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13107216358184814},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11739948391914368}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6528669595718384},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5692840218544006},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5210391879081726},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.5097629427909851},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5053656697273254},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5012476444244385},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.42397454380989075},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3565092086791992},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2887153625488281},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2634925842285156},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15114876627922058},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13107216358184814},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11739948391914368},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts189","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1641/48872190/bioinformatics_28_12_1641.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22513994","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22513994","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts189","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1641/48872190/bioinformatics_28_12_1641.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2136090938.pdf","grobid_xml":"https://content.openalex.org/works/W2136090938.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1973931828","https://openalex.org/W2133425807","https://openalex.org/W2135046866"],"related_works":["https://openalex.org/W4389426664","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W3198565742","https://openalex.org/W2010064959","https://openalex.org/W2157390150","https://openalex.org/W2119742499","https://openalex.org/W1985266044","https://openalex.org/W4387011503"],"abstract_inverted_index":{"The":[0],"R":[1],"package":[2],"TSSi":[3],"is":[4],"available":[5],"from":[6],"the":[7],"Bioconductor":[8],"web":[9],"site:":[10],"www.bioconductor.org/packages/release/bioc/html/TSSi.html.":[11]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
