{"id":"https://openalex.org/W2161318011","doi":"https://doi.org/10.1093/bioinformatics/btt015","title":"Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression","display_name":"Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression","publication_year":2013,"publication_date":"2013-01-12","ids":{"openalex":"https://openalex.org/W2161318011","doi":"https://doi.org/10.1093/bioinformatics/btt015","mag":"2161318011","pmid":"https://pubmed.ncbi.nlm.nih.gov/23314327"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt015","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/656/50335895/bioinformatics_29_5_656.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/29/5/656/50335895/bioinformatics_29_5_656.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001420352","display_name":"Michele Busby","orcid":"https://orcid.org/0000-0003-1731-288X"},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michele A. Busby","raw_affiliation_strings":["Department of Biology, Boston College, Chestnut Hill, MA 02467, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Boston College, Chestnut Hill, MA 02467, USA","institution_ids":["https://openalex.org/I103531236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003120045","display_name":"Chip Stewart","orcid":"https://orcid.org/0000-0003-2245-9552"},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chip Stewart","raw_affiliation_strings":["Department of Biology, Boston College, Chestnut Hill, MA 02467, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Boston College, Chestnut Hill, MA 02467, USA","institution_ids":["https://openalex.org/I103531236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103882008","display_name":"Chase Miller","orcid":null},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chase A. Miller","raw_affiliation_strings":["Department of Biology, Boston College, Chestnut Hill, MA 02467, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Boston College, Chestnut Hill, MA 02467, USA","institution_ids":["https://openalex.org/I103531236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037350846","display_name":"Krzysztof R. Grz\u0229da","orcid":null},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Krzysztof R. Grzeda","raw_affiliation_strings":["Department of Biology, Boston College, Chestnut Hill, MA 02467, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Boston College, Chestnut Hill, MA 02467, USA","institution_ids":["https://openalex.org/I103531236"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000369565","display_name":"G\u00e1bor Marth","orcid":"https://orcid.org/0000-0003-0222-1694"},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabor T. Marth","raw_affiliation_strings":["Department of Biology, Boston College, Chestnut Hill, MA 02467, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Boston College, Chestnut Hill, MA 02467, USA","institution_ids":["https://openalex.org/I103531236"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5001420352"],"corresponding_institution_ids":["https://openalex.org/I103531236"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":6.2891,"has_fulltext":true,"cited_by_count":144,"citation_normalized_percentile":{"value":0.97354739,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"29","issue":"5","first_page":"656","last_page":"657"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9958999752998352,"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":0.9940999746322632,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.49430418014526367},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46062296628952026},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4218071699142456},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.4147213101387024},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3465195298194885},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2876300513744354},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2343817949295044},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2327340841293335},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.1356886327266693},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13466838002204895},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12732630968093872}],"concepts":[{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.49430418014526367},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46062296628952026},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4218071699142456},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.4147213101387024},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3465195298194885},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2876300513744354},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2343817949295044},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2327340841293335},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.1356886327266693},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13466838002204895},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12732630968093872},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"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":"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":"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:10.1093/bioinformatics/btt015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt015","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/656/50335895/bioinformatics_29_5_656.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:23314327","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23314327","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},{"id":"pmh:oai:europepmc.org:2919510","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3582267","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3582267","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3582267","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt015","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt015","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/656/50335895/bioinformatics_29_5_656.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/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161318011.pdf","grobid_xml":"https://content.openalex.org/works/W2161318011.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W1578032204","https://openalex.org/W2110596109","https://openalex.org/W2152239989","https://openalex.org/W2155371242","https://openalex.org/W2171980444"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"Scotty":[0],"can":[1],"be":[2],"freely":[3],"accessed":[4],"on":[5],"the":[6],"web":[7],"at":[8],"http://euler.bc.edu/marthlab/scotty/scotty.php":[9]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":16},{"year":2018,"cited_by_count":18},{"year":2017,"cited_by_count":19},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
