{"id":"https://openalex.org/W1942153756","doi":"https://doi.org/10.1186/1471-2105-14-s7-s10","title":"NGS-Trex: Next Generation Sequencing Transcriptome profile explorer","display_name":"NGS-Trex: Next Generation Sequencing Transcriptome profile explorer","publication_year":2013,"publication_date":"2013-04-01","ids":{"openalex":"https://openalex.org/W1942153756","doi":"https://doi.org/10.1186/1471-2105-14-s7-s10","mag":"1942153756","pmid":"https://pubmed.ncbi.nlm.nih.gov/23815181"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-s7-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s7-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S7-S10","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/10.1186/1471-2105-14-S7-S10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089140700","display_name":"Ilenia Boria","orcid":null},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Ilenia Boria","raw_affiliation_strings":["Dipartimento di Chimica, Universit\u00e0 degli Studi di Milano, Milano, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica, Universit\u00e0 degli Studi di Milano, Milano, Italy","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053940021","display_name":"Lara Boatti","orcid":null},"institutions":[{"id":"https://openalex.org/I123338534","display_name":"Universit\u00e0 degli Studi del Piemonte Orientale \u201cAmedeo Avogadro\u201d","ror":"https://ror.org/04387x656","country_code":"IT","type":"education","lineage":["https://openalex.org/I123338534"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Lara Boatti","raw_affiliation_strings":["Dipartimento di Scienze e Innovazione Tecnologica, Universit\u00e0 del Piemonte Orientale, Alessandria, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Scienze e Innovazione Tecnologica, Universit\u00e0 del Piemonte Orientale, Alessandria, Italy","institution_ids":["https://openalex.org/I123338534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005312066","display_name":"Graziano Pesole","orcid":"https://orcid.org/0000-0003-3663-0859"},"institutions":[{"id":"https://openalex.org/I4210148743","display_name":"Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies","ror":"https://ror.org/05nzf7q96","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210148743","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I5561750","display_name":"University of Bari Aldo Moro","ror":"https://ror.org/027ynra39","country_code":"IT","type":"education","lineage":["https://openalex.org/I5561750"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Graziano Pesole","raw_affiliation_strings":["Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Universit\u00e0 degli Studi di Bari \"A. Moro\", Bari, Italy","Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Universit\u00e0 degli Studi di Bari \"A. Moro\", Bari, Italy","institution_ids":["https://openalex.org/I5561750"]},{"raw_affiliation_string":"Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy","institution_ids":["https://openalex.org/I4210148743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048693547","display_name":"Flavio Mignone","orcid":"https://orcid.org/0000-0002-4437-7817"},"institutions":[{"id":"https://openalex.org/I123338534","display_name":"Universit\u00e0 degli Studi del Piemonte Orientale \u201cAmedeo Avogadro\u201d","ror":"https://ror.org/04387x656","country_code":"IT","type":"education","lineage":["https://openalex.org/I123338534"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Flavio Mignone","raw_affiliation_strings":["Dipartimento di Scienze e Innovazione Tecnologica, Universit\u00e0 del Piemonte Orientale, Alessandria, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Scienze e Innovazione Tecnologica, Universit\u00e0 del Piemonte Orientale, Alessandria, Italy","institution_ids":["https://openalex.org/I123338534"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5048693547"],"corresponding_institution_ids":["https://openalex.org/I123338534"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.5139,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.81244148,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"14","issue":"S7","first_page":"S10","last_page":"S10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.6729999780654907,"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":0.6729999780654907,"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/T11482","display_name":"RNA modifications and cancer","score":0.06270000338554382,"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":0.05220000073313713,"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/upload","display_name":"Upload","score":0.7433592677116394},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6051873564720154},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5683322548866272},{"id":"https://openalex.org/keywords/massive-parallel-sequencing","display_name":"Massive parallel sequencing","score":0.5607544779777527},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5450918078422546},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5437695980072021},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4729052782058716},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4716821312904358},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4433956444263458},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.44061192870140076},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4294658303260803},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.4262404441833496},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.381714403629303},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.34614598751068115},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3139408826828003},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24563878774642944},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.22303512692451477},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20640406012535095},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.1798093020915985},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09153661131858826}],"concepts":[{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.7433592677116394},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6051873564720154},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5683322548866272},{"id":"https://openalex.org/C192800701","wikidata":"https://www.wikidata.org/wiki/Q6784807","display_name":"Massive parallel sequencing","level":4,"score":0.5607544779777527},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5450918078422546},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5437695980072021},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4729052782058716},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4716821312904358},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4433956444263458},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.44061192870140076},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4294658303260803},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.4262404441833496},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.381714403629303},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.34614598751068115},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3139408826828003},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24563878774642944},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.22303512692451477},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20640406012535095},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.1798093020915985},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09153661131858826}],"mesh":[{"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-14-s7-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s7-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S7-S10","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:23815181","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23815181","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:air.unimi.it:2434/255961","is_oa":true,"landing_page_url":"http://hdl.handle.net/2434/255961","pdf_url":null,"source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2631482","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3633008","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:ricerca.uniba.it:11586/64246","is_oa":false,"landing_page_url":"http://hdl.handle.net/11586/64246","pdf_url":null,"source":{"id":"https://openalex.org/S4377196296","display_name":"CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5561750","host_organization_name":"University of Bari Aldo Moro","host_organization_lineage":["https://openalex.org/I5561750"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-s7-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s7-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S7-S10","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":[{"display_name":"Industry, innovation and infrastructure","score":0.6200000047683716,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1254764628","display_name":null,"funder_award_id":"PRIN 2009","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G2655469437","display_name":null,"funder_award_id":"PNR-CNR Aging Program 2012\u20132014","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G2943443013","display_name":null,"funder_award_id":"PNR-CNR Aging Program 2012-2014","funder_id":"https://openalex.org/F4320322651","funder_display_name":"Consiglio Nazionale delle Ricerche"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320322651","display_name":"Consiglio Nazionale delle Ricerche","ror":"https://ror.org/04zaypm56"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1942153756.pdf","grobid_xml":"https://content.openalex.org/works/W1942153756.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1967358836","https://openalex.org/W1968458420","https://openalex.org/W1986657646","https://openalex.org/W1995070233","https://openalex.org/W2058805572","https://openalex.org/W2097065948","https://openalex.org/W2106678197","https://openalex.org/W2114405789","https://openalex.org/W2119298573","https://openalex.org/W2136482257"],"related_works":["https://openalex.org/W4283646568","https://openalex.org/W2052664817","https://openalex.org/W4229794866","https://openalex.org/W2105071916","https://openalex.org/W4243357985","https://openalex.org/W189065216","https://openalex.org/W1976142521","https://openalex.org/W4383032973","https://openalex.org/W2906188169","https://openalex.org/W2953068997"],"abstract_inverted_index":{"BACKGROUND:":[0],"Next-Generation":[1],"Sequencing":[2],"(NGS)":[3],"technology":[4],"has":[5],"exceptionally":[6],"increased":[7],"the":[8,32,59,71,82,98,120,149,162,166,174,197,207,240,244],"ability":[9],"to":[10,53,86,89,94,119,151,172,182,221,258,272],"sequence":[11],"DNA":[12],"in":[13,70],"a":[14,142,234,249],"massively":[15],"parallel":[16],"and":[17,27,48,61,66,93,105,147,155,189,218],"cost-effective":[18],"manner.":[19],"Nevertheless,":[20],"NGS":[21,123,282],"data":[22,96,124,254,269],"analysis":[23,121,175,255],"requires":[24],"bioinformatics":[25,103,264],"skills":[26],"computational":[28],"resources":[29],"well":[30],"beyond":[31],"possibilities":[33],"of":[34,41,63,84,101,122,161,168,200,212,243,276,281],"many":[35],"\"wet":[36,259],"biology\"":[37,260],"laboratories.":[38],"Moreover,":[39],"most":[40],"projects":[42,77],"only":[43],"require":[44],"few":[45,169],"sequencing":[46],"cycles":[47],"standard":[49],"tools":[50,271],"or":[51,232],"workflows":[52],"carry":[54],"out":[55],"suitable":[56],"analyses":[57],"for":[58,252],"identification":[60],"annotation":[62],"genes,":[64,213],"transcripts":[65],"splice":[67,215],"variants":[68],"found":[69],"biological":[72],"samples":[73,277],"under":[74],"investigation.":[75],"These":[76],"can":[78,209,225],"take":[79],"benefits":[80],"from":[81,126],"availability":[83],"easy":[85],"use":[87],"systems":[88],"automatically":[90],"analyse":[91],"sequences":[92,154],"mine":[95],"without":[97],"preventive":[99],"need":[100],"strong":[102],"background":[104],"hardware":[106],"infrastructure.":[107],"RESULTS:":[108],"To":[109],"address":[110],"this":[111],"issue":[112],"we":[113,132],"developed":[114],"an":[115,158],"automatic":[116],"system":[117,178],"targeted":[118,257],"obtained":[125],"large-scale":[127],"transcriptome":[128,163,274],"studies.":[129],"This":[130],"system,":[131],"named":[133],"NGS-Trex":[134,247],"(NGS":[135],"Transcriptome":[136],"profile":[137,164,199],"explorer)":[138],"is":[139,179,248],"available":[140],"through":[141,233],"simple":[143,204,235,250,268],"web":[144],"interface":[145],"http://www.ngs-trex.org":[146],"allows":[148],"user":[150,208],"upload":[152],"raw":[153],"easily":[156],"obtain":[157,210],"accurate":[159],"characterization":[160],"after":[165],"setting":[167],"parameters":[170],"required":[171],"tune":[173],"procedure.":[176],"The":[177],"also":[180],"able":[181],"assess":[183],"differential":[184],"expression":[185,198],"at":[186],"both":[187],"gene":[188],"transcript":[190],"level":[191],"(i.e.":[192],"splicing":[193],"isoforms)":[194],"by":[195],"comparing":[196],"different":[201],"samples.By":[202],"using":[203],"query":[205],"forms":[206],"list":[211],"transcripts,":[214],"sites":[216],"ranked":[217],"filtered":[219],"according":[220],"several":[222],"criteria.":[223],"Data":[224],"be":[226],"viewed":[227],"as":[228],"tables,":[229],"text":[230],"files":[231],"genome":[236],"browser":[237],"which":[238],"helps":[239],"visual":[241],"inspection":[242],"data.":[245],"CONCLUSIONS:":[246],"tool":[251],"RNA-Seq":[253],"mainly":[256],"researchers":[261],"with":[262],"limited":[263],"skills.":[265],"It":[266],"offers":[267],"mining":[270],"explore":[273],"profiles":[275],"investigated":[278],"taking":[279],"advantage":[280],"technologies.":[283]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
