{"id":"https://openalex.org/W4205133023","doi":"https://doi.org/10.1142/s0219720022500019","title":"Optimized splitting of mixed-species RNA sequencing data","display_name":"Optimized splitting of mixed-species RNA sequencing data","publication_year":2022,"publication_date":"2022-01-06","ids":{"openalex":"https://openalex.org/W4205133023","doi":"https://doi.org/10.1142/s0219720022500019","pmid":"https://pubmed.ncbi.nlm.nih.gov/34991436"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720022500019","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720022500019","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9081140","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Xuan Song","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xuan Song","raw_affiliation_strings":["Department of Neurology, Alzheimer\u2019s Disease Research Center, University of Pittsburgh, Pittsburgh, PA 15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology, Alzheimer\u2019s Disease Research Center, University of Pittsburgh, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hai Yun Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hai Yun Gao","raw_affiliation_strings":["Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, NJ 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Karl Herrup","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karl Herrup","raw_affiliation_strings":["Department of Neurology, Alzheimer\u2019s Disease Research Center, University of Pittsburgh, Pittsburgh, PA 15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology, Alzheimer\u2019s Disease Research Center, University of Pittsburgh, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":null,"display_name":"Ronald P. Hart","orcid":"https://orcid.org/0000-0003-4836-8712"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ronald P. Hart","raw_affiliation_strings":["Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, NJ 08854, USA"],"raw_orcid":"https://orcid.org/0000-0003-4836-8712","affiliations":[{"raw_affiliation_string":"Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, NJ 08854, USA","institution_ids":["https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1679,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.43991189,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"20","issue":"02","first_page":"2250001","last_page":"2250001"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6137999892234802,"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":0.6137999892234802,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.13779999315738678,"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/T10885","display_name":"Gene expression and cancer classification","score":0.03269999846816063,"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-sequencing","display_name":"DNA sequencing","score":0.5188000202178955},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5062000155448914},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.505299985408783},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.4465000033378601},{"id":"https://openalex.org/keywords/k-mer","display_name":"k-mer","score":0.4056999981403351},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.40230000019073486},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.3993000090122223},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37439998984336853}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6607000231742859},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5188000202178955},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5062000155448914},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.505299985408783},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.4465000033378601},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4392000138759613},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.412200003862381},{"id":"https://openalex.org/C2279292","wikidata":"https://www.wikidata.org/wiki/Q6322851","display_name":"k-mer","level":4,"score":0.4056999981403351},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.40230000019073486},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.3993000090122223},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37439998984336853},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.34459999203681946},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.33169999718666077},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3089999854564667},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.28949999809265137},{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.2867000102996826},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2750999927520752},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.27390000224113464},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2736999988555908},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.26930001378059387},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.25859999656677246},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.25609999895095825},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.25440001487731934},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.2531999945640564}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1142/s0219720022500019","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720022500019","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:34991436","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34991436","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9081140","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9081140","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,"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":"J Bioinform Comput Biol","raw_type":"Text"},{"id":"pmh:oai:repository.hkust.edu.hk:1783.1-159918","is_oa":false,"landing_page_url":"http://repository.hkust.edu.hk/ir/Record/1783.1-159918","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"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"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9081140","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9081140","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,"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":"J Bioinform Comput Biol","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1083756078","display_name":null,"funder_award_id":"U10AA008401","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G2697108588","display_name":null,"funder_award_id":"R01ES026057","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G320220334","display_name":null,"funder_award_id":"R01 ES026057","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G7894658358","display_name":null,"funder_award_id":"U24 AG021886","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G8073654373","display_name":null,"funder_award_id":"U10 AA008401","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"}],"funders":[{"id":"https://openalex.org/F4320337330","display_name":"National Institute on Alcohol Abuse and Alcoholism","ror":"https://ror.org/02jzrsm59"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W188558181","https://openalex.org/W1524680991","https://openalex.org/W1601963269","https://openalex.org/W1679661372","https://openalex.org/W1950136256","https://openalex.org/W1964980861","https://openalex.org/W1975799894","https://openalex.org/W1985987855","https://openalex.org/W1991909246","https://openalex.org/W1995363983","https://openalex.org/W2023652080","https://openalex.org/W2049491375","https://openalex.org/W2055911634","https://openalex.org/W2073162672","https://openalex.org/W2074772891","https://openalex.org/W2095546080","https://openalex.org/W2120615054","https://openalex.org/W2121016876","https://openalex.org/W2135621733","https://openalex.org/W2135957529","https://openalex.org/W2138111534","https://openalex.org/W2141638474","https://openalex.org/W2151464048","https://openalex.org/W2151831732","https://openalex.org/W2154775341","https://openalex.org/W2161136893","https://openalex.org/W2161381512","https://openalex.org/W2170112692","https://openalex.org/W2186845332","https://openalex.org/W2224056471","https://openalex.org/W2274866051","https://openalex.org/W2323326409","https://openalex.org/W2503964676","https://openalex.org/W2523620612","https://openalex.org/W2527699779","https://openalex.org/W2561206810","https://openalex.org/W2590949976","https://openalex.org/W2745359018","https://openalex.org/W2785495390","https://openalex.org/W2789876780","https://openalex.org/W2790756470","https://openalex.org/W2797372563","https://openalex.org/W2805033630","https://openalex.org/W2889587233","https://openalex.org/W2896969435","https://openalex.org/W2901268286","https://openalex.org/W2909430042","https://openalex.org/W2913942704","https://openalex.org/W2915445509","https://openalex.org/W2940844549","https://openalex.org/W2951890476","https://openalex.org/W2952898185","https://openalex.org/W2955793676","https://openalex.org/W2964101377","https://openalex.org/W2971426566","https://openalex.org/W2981190305","https://openalex.org/W2998840182","https://openalex.org/W3023192521","https://openalex.org/W3033406782","https://openalex.org/W3034083044","https://openalex.org/W3036610605","https://openalex.org/W3095136801"],"related_works":[],"abstract_inverted_index":{"Gene":[0],"expression":[1],"studies":[2],"using":[3],"xenograft":[4],"transplants":[5],"or":[6,27],"co-culture":[7],"systems,":[8],"usually":[9],"with":[10,87,122,131,166],"mixed":[11],"human":[12,135],"and":[13,59,136],"mouse":[14,137],"cells,":[15],"have":[16],"proven":[17],"to":[18,21,65,78,161],"be":[19,162],"valuable":[20],"uncover":[22],"cellular":[23],"dynamics":[24],"during":[25],"development":[26],"in":[28],"disease":[29],"models.":[30],"However,":[31],"the":[32,110,163],"mRNA":[33],"sequence":[34],"similarities":[35],"among":[36],"species":[37,99],"presents":[38],"a":[39,66,96,147],"challenge":[40],"for":[41,49],"accurate":[42],"transcript":[43],"quantification.":[44],"To":[45],"identify":[46],"optimal":[47,74],"strategies":[48,141],"analyzing":[50],"mixed-species":[51],"RNA":[52,119],"sequencing":[53,80,120],"data,":[54],"we":[55],"evaluate":[56],"both":[57,127],"alignment-dependent":[58],"alignment-independent":[60],"methods.":[61],"Alignment":[62],"of":[63,98,113,134,151,158],"reads":[64,81,121,144,159],"pooled":[67],"reference":[68],"index":[69],"is":[70],"effective,":[71],"particularly":[72],"if":[73],"alignments":[75],"are":[76,85],"used":[77],"classify":[79,118],"by":[82,145,155],"species,":[83,117,146],"which":[84,108],"re-aligned":[86],"individual":[88],"genomes,":[89],"generating":[90],"[Formula:":[91],"see":[92],"text]":[93],"accuracy":[94],"across":[95],"range":[97],"ratios.":[100],"Alignment-independent":[101],"methods,":[102],"such":[103],"as":[104],"convolutional":[105],"neural":[106],"networks,":[107],"extract":[109],"conserved":[111],"patterns":[112],"sequences":[114],"from":[115],"two":[116],"over":[123],"85%":[124],"accuracy.":[125],"Importantly,":[126],"methods":[128],"perform":[129],"well":[130],"different":[132],"ratios":[133],"reads.":[138],"While":[139],"non-alignment":[140],"successfully":[142],"partitioned":[143],"more":[148,164],"traditional":[149],"approach":[150],"mixed-genome":[152],"alignment":[153],"followed":[154],"optimized":[156],"separation":[157],"proved":[160],"successful":[165],"lower":[167],"error":[168],"rates.":[169]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2022-01-26T00:00:00"}