{"id":"https://openalex.org/W3016755693","doi":"https://doi.org/10.1186/s12859-020-3484-z","title":"Short paired-end reads trump long single-end reads for expression analysis","display_name":"Short paired-end reads trump long single-end reads for expression analysis","publication_year":2020,"publication_date":"2020-04-19","ids":{"openalex":"https://openalex.org/W3016755693","doi":"https://doi.org/10.1186/s12859-020-3484-z","mag":"3016755693","pmid":"https://pubmed.ncbi.nlm.nih.gov/32306895"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-3484-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3484-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3484-z","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/track/pdf/10.1186/s12859-020-3484-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015348635","display_name":"Adam H. Freedman","orcid":"https://orcid.org/0000-0003-4714-3925"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam H. Freedman","raw_affiliation_strings":["Informatics Group, Harvard University, Cambridge, MA, 02138, USA"],"affiliations":[{"raw_affiliation_string":"Informatics Group, Harvard University, Cambridge, MA, 02138, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101748742","display_name":"John M. Gaspar","orcid":"https://orcid.org/0000-0002-0155-4123"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John M. Gaspar","raw_affiliation_strings":["Informatics Group, Harvard University, Cambridge, MA, 02138, USA"],"affiliations":[{"raw_affiliation_string":"Informatics Group, Harvard University, Cambridge, MA, 02138, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015705059","display_name":"Timothy B. Sackton","orcid":"https://orcid.org/0000-0003-1673-9216"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy B. Sackton","raw_affiliation_strings":["Informatics Group, Harvard University, Cambridge, MA, 02138, USA. tsackton@g.harvard.edu","Informatics Group, Harvard University, Cambridge, MA, 02138, USA"],"affiliations":[{"raw_affiliation_string":"Informatics Group, Harvard University, Cambridge, MA, 02138, USA. tsackton@g.harvard.edu","institution_ids":[]},{"raw_affiliation_string":"Informatics Group, Harvard University, Cambridge, MA, 02138, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5015348635"],"corresponding_institution_ids":["https://openalex.org/I136199984"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.1171,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.74303648,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"21","issue":"1","first_page":"149","last_page":"149"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9970999956130981,"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/T11970","display_name":"Molecular Biology Techniques and Applications","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/dna-microarray","display_name":"DNA microarray","score":0.5469574332237244},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5373410582542419},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46086016297340393},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44426265358924866},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.44028547406196594},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.43732383847236633},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41777151823043823},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4002348482608795},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3498404920101166}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5469574332237244},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5373410582542419},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46086016297340393},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44426265358924866},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.44028547406196594},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.43732383847236633},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41777151823043823},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4002348482608795},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3498404920101166},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-020-3484-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3484-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3484-z","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:32306895","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32306895","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:doaj.org/article:ec4b6f7fa9644b899767bee2b0221432","is_oa":true,"landing_page_url":"https://doaj.org/article/ec4b6f7fa9644b899767bee2b0221432","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":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-11 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7168855","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7168855","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-3484-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3484-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3484-z","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309622","display_name":"Harvard University","ror":"https://ror.org/03vek6s52"},{"id":"https://openalex.org/F4320338027","display_name":"FAS Division of Science, Harvard University","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3016755693.pdf","grobid_xml":"https://content.openalex.org/works/W3016755693.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1976848056","https://openalex.org/W1983275320","https://openalex.org/W1999574084","https://openalex.org/W2068614693","https://openalex.org/W2074414424","https://openalex.org/W2127372456","https://openalex.org/W2133237718","https://openalex.org/W2137526110","https://openalex.org/W2151462466","https://openalex.org/W2161106528","https://openalex.org/W2170551349","https://openalex.org/W2179438025","https://openalex.org/W2197124664","https://openalex.org/W2287064828","https://openalex.org/W2310622210","https://openalex.org/W2323326409","https://openalex.org/W2547794687","https://openalex.org/W2620721366","https://openalex.org/W2744970791","https://openalex.org/W2885204059","https://openalex.org/W2904592340","https://openalex.org/W2904884010","https://openalex.org/W2951781413","https://openalex.org/W2951899931","https://openalex.org/W2953075187","https://openalex.org/W2969369031"],"related_works":["https://openalex.org/W2392243736","https://openalex.org/W86652014","https://openalex.org/W106077234","https://openalex.org/W2041374557","https://openalex.org/W2081929287","https://openalex.org/W2144348650","https://openalex.org/W2132561013","https://openalex.org/W1994852842","https://openalex.org/W4246178523","https://openalex.org/W1902990570"],"abstract_inverted_index":{"Researchers":[0],"seeking":[1],"a":[2,15],"cost-effective":[3],"approach":[4],"for":[5],"gene-level":[6],"expression":[7,27,31],"analysis":[8],"should":[9],"prefer":[10],"short":[11],"paired-end":[12,20],"reads":[13,21],"over":[14],"longer":[16],"single-end":[17],"strategy.":[18],"Short":[19],"will":[22],"also":[23],"give":[24],"reasonably":[25],"robust":[26],"estimates":[28],"and":[29],"differential":[30],"results":[32],"at":[33],"the":[34],"isoform":[35],"level.":[36]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}