{"id":"https://openalex.org/W1996454352","doi":"https://doi.org/10.1371/journal.pone.0076144","title":"The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing","display_name":"The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing","publication_year":2013,"publication_date":"2013-09-26","ids":{"openalex":"https://openalex.org/W1996454352","doi":"https://doi.org/10.1371/journal.pone.0076144","mag":"1996454352","pmid":"https://pubmed.ncbi.nlm.nih.gov/24086702"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pone.0076144","doi":"https://doi.org/10.1371/journal.pone.0076144","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0076144","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0076144&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS ONE","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0076144&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021652536","display_name":"Toon Rosseel","orcid":"https://orcid.org/0000-0002-8155-3197","observed_orcids":["https://orcid.org/0000-0002-8155-3197"]},"institutions":[{"id":"https://openalex.org/I4210108698","display_name":"Veterinary and Agrochemical Research Centre","ror":"https://ror.org/0153sam53","country_code":"BE","type":"facility","lineage":["https://openalex.org/I4210108698"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Toon Rosseel","raw_affiliation_strings":["Operational Directorate of Virology, Veterinary and Agrochemical Research Centre, Ukkel, Brussels, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Operational Directorate of Virology, Veterinary and Agrochemical Research Centre, Ukkel, Brussels, Belgium","institution_ids":["https://openalex.org/I4210108698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034362684","display_name":"Steven Van Borm","orcid":"https://orcid.org/0000-0002-3464-2306","observed_orcids":["https://orcid.org/0000-0002-3464-2306"]},"institutions":[{"id":"https://openalex.org/I4210108698","display_name":"Veterinary and Agrochemical Research Centre","ror":"https://ror.org/0153sam53","country_code":"BE","type":"facility","lineage":["https://openalex.org/I4210108698"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Steven Van Borm","raw_affiliation_strings":["Operational Directorate of Virology, Veterinary and Agrochemical Research Centre, Ukkel, Brussels, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Operational Directorate of Virology, Veterinary and Agrochemical Research Centre, Ukkel, Brussels, Belgium","institution_ids":["https://openalex.org/I4210108698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061772820","display_name":"Frank Vandenbussche","orcid":"https://orcid.org/0000-0002-3214-6763","observed_orcids":["https://orcid.org/0000-0002-3214-6763"]},"institutions":[{"id":"https://openalex.org/I4210108698","display_name":"Veterinary and Agrochemical Research Centre","ror":"https://ror.org/0153sam53","country_code":"BE","type":"facility","lineage":["https://openalex.org/I4210108698"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Frank Vandenbussche","raw_affiliation_strings":["Operational Directorate of Virology, Veterinary and Agrochemical Research Centre, Ukkel, Brussels, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Operational Directorate of Virology, Veterinary and Agrochemical Research Centre, Ukkel, Brussels, Belgium","institution_ids":["https://openalex.org/I4210108698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064611708","display_name":"Bernd Hoffmann","orcid":"https://orcid.org/0000-0001-5358-6445","observed_orcids":["https://orcid.org/0000-0001-5358-6445"]},"institutions":[{"id":"https://openalex.org/I1310048521","display_name":"Friedrich-Loeffler-Institut","ror":"https://ror.org/025fw7a54","country_code":"DE","type":"government","lineage":["https://openalex.org/I1310048521","https://openalex.org/I2801963157"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bernd Hoffmann","raw_affiliation_strings":["Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany","Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany","institution_ids":["https://openalex.org/I1310048521"]},{"raw_affiliation_string":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany","institution_ids":["https://openalex.org/I1310048521"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103474702","display_name":"Thierry van den Berg","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210108698","display_name":"Veterinary and Agrochemical Research Centre","ror":"https://ror.org/0153sam53","country_code":"BE","type":"facility","lineage":["https://openalex.org/I4210108698"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Thierry van den Berg","raw_affiliation_strings":["Operational Directorate of Virology, Veterinary and Agrochemical Research Centre, Ukkel, Brussels, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Operational Directorate of Virology, Veterinary and Agrochemical Research Centre, Ukkel, Brussels, Belgium","institution_ids":["https://openalex.org/I4210108698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036973907","display_name":"Martin Beer","orcid":"https://orcid.org/0000-0002-0598-5254","observed_orcids":["https://orcid.org/0000-0002-0598-5254"]},"institutions":[{"id":"https://openalex.org/I1310048521","display_name":"Friedrich-Loeffler-Institut","ror":"https://ror.org/025fw7a54","country_code":"DE","type":"government","lineage":["https://openalex.org/I1310048521","https://openalex.org/I2801963157"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Beer","raw_affiliation_strings":["Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany","Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany","institution_ids":["https://openalex.org/I1310048521"]},{"raw_affiliation_string":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany","institution_ids":["https://openalex.org/I1310048521"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056334251","display_name":"Dirk W. H\u00f6per","orcid":"https://orcid.org/0000-0001-8408-2274","observed_orcids":["https://orcid.org/0000-0001-8408-2274"]},"institutions":[{"id":"https://openalex.org/I1310048521","display_name":"Friedrich-Loeffler-Institut","ror":"https://ror.org/025fw7a54","country_code":"DE","type":"government","lineage":["https://openalex.org/I1310048521","https://openalex.org/I2801963157"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dirk H\u00f6per","raw_affiliation_strings":["Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany","Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany","institution_ids":["https://openalex.org/I1310048521"]},{"raw_affiliation_string":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany","institution_ids":["https://openalex.org/I1310048521"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5034362684"],"corresponding_institution_ids":["https://openalex.org/I4210108698"],"apc_list":{"value":2382,"currency":"USD","value_usd":2382},"apc_paid":{"value":2382,"currency":"USD","value_usd":2382},"fwci":3.6299,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.93843049,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"8","issue":"9","first_page":"e76144","last_page":"e76144"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9717000126838684,"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":0.9717000126838684,"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":0.01360000018030405,"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":0.0024999999441206455,"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/rna-secondary-structure","display_name":"RNA secondary structure","score":0.7689999938011169},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC content","score":0.890999972820282},{"id":"https://openalex.org/keywords/viral-rna-sequencing","display_name":"viral RNA sequencing","score":0.722000002861023},{"id":"https://openalex.org/keywords/viral-metagenomics","display_name":"viral metagenomics","score":0.8330000042915344},{"id":"https://openalex.org/keywords/massive-parallel-sequencing","display_name":"massive parallel sequencing","score":0.5770000219345093}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6395859122276306},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.617664635181427},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.6169910430908203},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5868824124336243},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5536500215530396},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5427510738372803},{"id":"https://openalex.org/C54985914","wikidata":"https://www.wikidata.org/wiki/Q1295754","display_name":"Consensus sequence","level":4,"score":0.5096440315246582},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4933532774448395},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.44838595390319824},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.444061815738678},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.43927890062332153},{"id":"https://openalex.org/C84148353","wikidata":"https://www.wikidata.org/wiki/Q863908","display_name":"Nucleic acid sequence","level":3,"score":0.4189123511314392},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3673549294471741},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18094795942306519},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.12682759761810303},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12341079115867615},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D014773","descriptor_name":"Virology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D014773","descriptor_name":"Virology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D014773","descriptor_name":"Virology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015982","descriptor_name":"Bias","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015982","descriptor_name":"Bias","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015982","descriptor_name":"Bias","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D018076","descriptor_name":"DNA, Complementary","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D018109","descriptor_name":"Avulavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018109","descriptor_name":"Avulavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018109","descriptor_name":"Avulavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D021141","descriptor_name":"Nucleic Acid Amplification Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021141","descriptor_name":"Nucleic Acid Amplification Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021141","descriptor_name":"Nucleic Acid Amplification Techniques","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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pone.0076144","doi":"https://doi.org/10.1371/journal.pone.0076144","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0076144","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0076144&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS ONE","raw_type":"journal-article"},{"id":"pmid:24086702","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24086702","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,"listed_in":[],"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":"PloS one","raw_type":"Journal Article"},{"id":"pmh:oai:archive.ugent.be:6715417","doi":null,"is_oa":true,"landing_page_url":"https://biblio.ugent.be/publication/6715417","pdf_url":"https://biblio.ugent.be/publication/6715417/file/6715431.pdf","source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"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":"ISSN: 1932-6203","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2781245","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3784409","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,"listed_in":[],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3784409","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3784409","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"PLoS One","raw_type":"Text"},{"id":"pmh:oai:www.openagrar.de:openagrar_mods_00002552","doi":null,"is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3784409","pdf_url":null,"source":{"id":"https://openalex.org/S7407055137","display_name":"OpenAgrar","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.811.7006","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.811.7006","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/08/59/pone.0076144.PMC3784409.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:604ac426192e48df8194e04d0adb18bc","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/604ac426192e48df8194e04d0adb18bc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS ONE, Vol 8, Iss 9, p e76144 (2013)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pone.0076144","doi":"https://doi.org/10.1371/journal.pone.0076144","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pone.0076144","pdf_url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0076144&type=printable","source":{"id":"https://openalex.org/S202381698","display_name":"PLoS ONE","issn_l":"1932-6203","issn":["1932-6203"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-c","doyens","erih-plus","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS ONE","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G7407665301","display_name":null,"funder_award_id":"01KI1016A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8897546876","display_name":"Coordination of European Research on Emerging and Major Infectious Diseases of Livestock","funder_award_id":"219235","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1996454352.pdf","grobid_xml":"https://content.openalex.org/works/W1996454352.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W5102173","https://openalex.org/W85954549","https://openalex.org/W1576737979","https://openalex.org/W1610919278","https://openalex.org/W1969522526","https://openalex.org/W1969867599","https://openalex.org/W1975175764","https://openalex.org/W1976705029","https://openalex.org/W1990926035","https://openalex.org/W1993080258","https://openalex.org/W2002700895","https://openalex.org/W2004572603","https://openalex.org/W2013642915","https://openalex.org/W2017593822","https://openalex.org/W2029401821","https://openalex.org/W2033602255","https://openalex.org/W2042704442","https://openalex.org/W2052733268","https://openalex.org/W2068507450","https://openalex.org/W2078626331","https://openalex.org/W2080486903","https://openalex.org/W2086561953","https://openalex.org/W2092155253","https://openalex.org/W2094918645","https://openalex.org/W2096605667","https://openalex.org/W2098407917","https://openalex.org/W2106638291","https://openalex.org/W2108166985","https://openalex.org/W2113419581","https://openalex.org/W2118526609","https://openalex.org/W2127883868","https://openalex.org/W2128114769","https://openalex.org/W2130164103","https://openalex.org/W2133856957","https://openalex.org/W2138190969","https://openalex.org/W2138270253","https://openalex.org/W2139122528","https://openalex.org/W2141040082","https://openalex.org/W2148497233","https://openalex.org/W2148914499","https://openalex.org/W2151520667","https://openalex.org/W2153520257","https://openalex.org/W2153848419","https://openalex.org/W2156776183","https://openalex.org/W2166582607","https://openalex.org/W2427977489","https://openalex.org/W2582743722"],"related_works":["https://openalex.org/W2087940846","https://openalex.org/W2444049591","https://openalex.org/W1981356107","https://openalex.org/W2036131961","https://openalex.org/W1987319986","https://openalex.org/W2093930804","https://openalex.org/W2156159819","https://openalex.org/W2348589365","https://openalex.org/W2383308243","https://openalex.org/W2214570915"],"abstract_inverted_index":{"Sequence":[0],"Independent":[1],"Single":[2],"Primer":[3],"Amplification":[4],"is":[5],"one":[6],"of":[7,27,68,79,119,138,186,226],"the":[8,69,74,85,120,135,139,143,147,151,184,187,200,224],"most":[9],"widely":[10],"used":[11,32,102],"random":[12,30,95,175,201,227],"amplification":[13,49,188,230],"approaches":[14],"in":[15,116,123,154,174,183,206],"virology":[16],"for":[17,44,236],"sequencing":[18,56],"template":[19],"preparation.":[20],"This":[21],"technique":[22],"relies":[23],"on":[24,115],"oligonucleotides":[25],"consisting":[26],"a":[28,39,65,104],"3'":[29,136],"part":[31,137],"to":[33,57,83,89,108,125,134,150,223],"prime":[34],"complementary":[35],"DNA":[36],"synthesis":[37],"and":[38,131,165,182,204,243],"5'":[40,216],"defined":[41,217],"tag":[42,140,144,218],"sequence":[43,71,91,121,132,145,155,185,203,209],"subsequent":[45],"amplification.":[46,96],"Recently,":[47],"this":[48,80,159],"method":[50],"was":[51,82,101],"combined":[52],"with":[53],"next":[54],"generation":[55],"obtain":[58],"viral":[59,167,241],"sequences.":[60,219],"However,":[61],"these":[62,110],"studies":[63],"showed":[64],"biased":[66,90],"distribution":[67],"resulting":[70],"reads":[72],"over":[73],"analyzed":[75],"genomes.":[76],"The":[77,190],"aim":[78],"study":[81],"elucidate":[84],"mechanisms":[86],"that":[87,142,232],"lead":[88],"depth":[92,122],"when":[93],"using":[94,162,214],"Avian":[97],"paramyxovirus":[98],"type":[99],"8":[100],"as":[103,169,171,240],"model":[105],"RNA":[106,128],"virus":[107],"investigate":[109],"mechanisms.":[111],"We":[112,157],"showed,":[113],"based":[114],"silico":[117,207],"analysis":[118],"relation":[124],"GC-content,":[126],"predicted":[127],"secondary":[129],"structure":[130],"complementarity":[133],"sequence,":[141],"has":[146],"main":[148],"contribution":[149],"observed":[152,191],"bias":[153,194],"depth.":[156],"confirmed":[158],"finding":[160],"experimentally":[161],"both":[163],"fragmented":[164],"non-fragmented":[166],"RNAs":[168],"well":[170],"primers":[172],"differing":[173],"oligomer":[176,202],"length":[177],"(6":[178],"or":[179],"12":[180],"nucleotides)":[181],"tag.":[189],"oligonucleotide":[192],"annealing":[193],"can":[195],"be":[196],"reduced":[197],"by":[198,205],"extending":[199],"combining":[208],"data":[210],"from":[211],"SISPA":[212],"experiments":[213],"different":[215],"These":[220],"findings":[221],"contribute":[222],"optimization":[225],"nucleic":[228],"acid":[229],"protocols":[231],"are":[233],"currently":[234],"required":[235],"downstream":[237],"applications":[238],"such":[239],"metagenomics":[242],"microarray":[244],"analysis.":[245]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":7},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":6}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2025-10-10T00:00:00"}