{"id":"https://openalex.org/W4225799922","doi":"https://doi.org/10.1093/bib/bbac195","title":"MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach","display_name":"MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach","publication_year":2022,"publication_date":"2022-04-28","ids":{"openalex":"https://openalex.org/W4225799922","doi":"https://doi.org/10.1093/bib/bbac195","pmid":"https://pubmed.ncbi.nlm.nih.gov/35580841"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac195","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac195","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102199603","display_name":"Hongyu Ding","orcid":"https://orcid.org/0009-0002-6331-5889"},"institutions":[{"id":"https://openalex.org/I4210166499","display_name":"Henan Polytechnic University","ror":"https://ror.org/05vr1c885","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210166499"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongyu Ding","raw_affiliation_strings":["College of Computer Science and Technology, Henan Polytechnic University , Jiaozuo, 454003, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Henan Polytechnic University , Jiaozuo, 454003, China","institution_ids":["https://openalex.org/I4210166499"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100422484","display_name":"Junwei Luo","orcid":"https://orcid.org/0000-0001-6841-9893"},"institutions":[{"id":"https://openalex.org/I4210166499","display_name":"Henan Polytechnic University","ror":"https://ror.org/05vr1c885","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210166499"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junwei Luo","raw_affiliation_strings":["College of Computer Science and Technology, Henan Polytechnic University , Jiaozuo, 454003, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Henan Polytechnic University , Jiaozuo, 454003, China","institution_ids":["https://openalex.org/I4210166499"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100422484"],"corresponding_institution_ids":["https://openalex.org/I4210166499"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.9065,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.86145863,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/genotyping","display_name":"Genotyping","score":0.8718765377998352},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6800875663757324},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6776233911514282},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6328201293945312},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6202306151390076},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5583740472793579},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4781004786491394},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4684586226940155},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4467846155166626},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.44148769974708557},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3784519135951996},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3632444739341736},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23161101341247559},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1951446235179901},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.15830984711647034},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12483006715774536}],"concepts":[{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.8718765377998352},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6800875663757324},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6776233911514282},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6328201293945312},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6202306151390076},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5583740472793579},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4781004786491394},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4684586226940155},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4467846155166626},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.44148769974708557},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3784519135951996},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3632444739341736},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23161101341247559},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1951446235179901},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.15830984711647034},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12483006715774536},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":"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":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060005","descriptor_name":"Genotyping Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac195","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac195","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35580841","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35580841","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G78415896","display_name":null,"funder_award_id":"61972134","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1912672559","https://openalex.org/W2002438422","https://openalex.org/W2137759177","https://openalex.org/W2141581393","https://openalex.org/W2141704631","https://openalex.org/W2148873746","https://openalex.org/W2396849069","https://openalex.org/W2482722766","https://openalex.org/W2582800429","https://openalex.org/W2789843538","https://openalex.org/W2901438556","https://openalex.org/W2908721251","https://openalex.org/W2948024819","https://openalex.org/W2949062400","https://openalex.org/W2950121474","https://openalex.org/W2951764279","https://openalex.org/W2963420686","https://openalex.org/W2990344913","https://openalex.org/W3032034316","https://openalex.org/W3034581902","https://openalex.org/W3046401484","https://openalex.org/W4394666350","https://openalex.org/W6674561012","https://openalex.org/W6743731764"],"related_works":["https://openalex.org/W4321369474","https://openalex.org/W4312417841","https://openalex.org/W3156786002","https://openalex.org/W4381487685","https://openalex.org/W2738221750","https://openalex.org/W564581980","https://openalex.org/W2337926734","https://openalex.org/W4366224123","https://openalex.org/W4320802194","https://openalex.org/W4381832759"],"abstract_inverted_index":{"Structural":[0],"variations":[1],"(SVs)":[2],"play":[3],"important":[4],"roles":[5],"in":[6,129],"human":[7],"genetic":[8,27],"diversity;":[9],"deletions":[10],"and":[11,32,54,76,80,87,94,127],"insertions":[12],"are":[13,57],"two":[14],"common":[15],"types":[16],"of":[17,51,90,131],"SVs":[18,34],"that":[19,43,61,121],"have":[20,47],"been":[21],"proven":[22],"to":[23,104],"be":[24],"associated":[25],"with":[26,109],"diseases.":[28],"Hence,":[29],"accurately":[30],"detecting":[31],"genotyping":[33,81],"is":[35,143],"significant":[36],"for":[37],"disease":[38],"research.":[39],"Despite":[40],"the":[41,49],"fact":[42],"long-read":[44,116],"sequencing":[45,117],"technologies":[46],"improved":[48],"field":[50],"SV":[52,78,107],"detection":[53,79,108],"genotyping,":[55],"there":[56],"still":[58],"some":[59],"challenges":[60],"prevent":[62],"satisfactory":[63],"results":[64],"from":[65,145],"being":[66],"obtained.":[67],"In":[68],"this":[69],"paper,":[70],"we":[71,119],"propose":[72],"MAMnet,":[73],"a":[74,88,100,110],"fast":[75],"scalable":[77],"method":[82],"based":[83],"on":[84],"long":[85,95],"reads":[86],"combination":[89],"convolutional":[91],"neural":[92,102],"network":[93,103],"short-term":[96],"network.":[97],"MAMnet":[98,122],"uses":[99],"deep":[101],"implement":[105],"sensitive":[106],"novel":[111],"prediction":[112],"strategy.":[113],"On":[114],"real":[115],"datasets,":[118],"demonstrate":[120],"outperforms":[123],"Sniffles,":[124],"SVIM,":[125],"cuteSV":[126],"PBSV":[128],"terms":[130],"their":[132],"F1":[133],"scores":[134],"while":[135],"achieving":[136],"better":[137],"scaling":[138],"performance.":[139],"The":[140],"source":[141],"code":[142],"available":[144],"https://github.com/micahvista/MAMnet.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}
