{"id":"https://openalex.org/W2092708422","doi":"https://doi.org/10.1109/bmei.2011.6098547","title":"A de novo assembly method for metagenomic DNA reads with mate pairs","display_name":"A de novo assembly method for metagenomic DNA reads with mate pairs","publication_year":2011,"publication_date":"2011-10-01","ids":{"openalex":"https://openalex.org/W2092708422","doi":"https://doi.org/10.1109/bmei.2011.6098547","mag":"2092708422"},"language":"en","primary_location":{"id":"doi:10.1109/bmei.2011.6098547","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bmei.2011.6098547","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5024277105","display_name":"Binbin Lai","orcid":"https://orcid.org/0000-0002-2831-2677"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Binbin Lai","raw_affiliation_strings":["State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, Center of Theoretical Biology of AAIS, Peking University, Beijing, China","State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Center for Theoretical Biology of AAIS, Peking University Beijing 100871, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, Center of Theoretical Biology of AAIS, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Center for Theoretical Biology of AAIS, Peking University Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000910958","display_name":"Ruogu Ding","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruogu Ding","raw_affiliation_strings":["State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, Center of Theoretical Biology of AAIS, Peking University, Beijing, China","State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Center for Theoretical Biology of AAIS, Peking University Beijing 100871, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, Center of Theoretical Biology of AAIS, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Center for Theoretical Biology of AAIS, Peking University Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060533782","display_name":"Huaiqiu Zhu","orcid":"https://orcid.org/0000-0002-6376-218X"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huaiqiu Zhu","raw_affiliation_strings":["State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, Center of Theoretical Biology of AAIS, Peking University, Beijing, China","State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Center for Theoretical Biology of AAIS, Peking University Beijing 100871, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, Center of Theoretical Biology of AAIS, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"State Key Lab for Turbulence and Complex Systems and Department of Biomedical Engineering, Peking University, Center for Theoretical Biology of AAIS, Peking University Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024277105"],"corresponding_institution_ids":["https://openalex.org/I20231570"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11464504,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"312","issue":null,"first_page":"1562","last_page":"1566"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9667999744415283,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.9402787089347839},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.9017094373703003},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.6652754545211792},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.6108384728431702},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.550043523311615},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4264855682849884},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4125276207923889},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41142538189888},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4032108783721924},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3992840349674225},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.29148030281066895},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2067962884902954},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17392924427986145},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.12338313460350037},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11274021863937378},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08735057711601257}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.9402787089347839},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9017094373703003},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.6652754545211792},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.6108384728431702},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.550043523311615},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4264855682849884},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4125276207923889},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41142538189888},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4032108783721924},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3992840349674225},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.29148030281066895},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2067962884902954},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17392924427986145},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.12338313460350037},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11274021863937378},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08735057711601257},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bmei.2011.6098547","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bmei.2011.6098547","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.44999998807907104}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1635391495","https://openalex.org/W2048673910","https://openalex.org/W2048818637","https://openalex.org/W2055503200","https://openalex.org/W2096634299","https://openalex.org/W2113601822","https://openalex.org/W2114133992","https://openalex.org/W2124637227","https://openalex.org/W2132415967","https://openalex.org/W2136651963","https://openalex.org/W2141217788","https://openalex.org/W2143074195","https://openalex.org/W2145317788","https://openalex.org/W2145336165","https://openalex.org/W2156104322","https://openalex.org/W2160969485","https://openalex.org/W2161668137","https://openalex.org/W2914081640"],"related_works":["https://openalex.org/W2330186985","https://openalex.org/W2950447380","https://openalex.org/W2345730070","https://openalex.org/W2055448750","https://openalex.org/W3134563641","https://openalex.org/W1986608492","https://openalex.org/W3165667290","https://openalex.org/W2028002954","https://openalex.org/W2154701173","https://openalex.org/W2152680529"],"abstract_inverted_index":{"A":[0],"high":[1],"quality":[2],"assembly":[3,51,102],"of":[4,18,31,43],"reads,":[5],"which":[6],"are":[7],"short":[8],"fragments":[9],"generated":[10],"from":[11,83],"shotgun":[12],"sequencing,":[13],"is":[14],"a":[15,48,112],"substantial":[16],"part":[17],"the":[19,32,37,41,77,84],"metagenome":[20,93],"projects.":[21],"Although":[22],"traditional":[23],"assemblers":[24],"have":[25],"been":[26],"employed":[27],"in":[28],"initial":[29],"analysis":[30],"metagenomes,":[33],"they":[34],"cannot":[35],"surmount":[36],"challenges":[38],"created":[39],"by":[40],"features":[42],"metagenomic":[44],"data.":[45],"We":[46],"present":[47],"de":[49],"novo":[50],"algorithm":[52,74],"for":[53],"metagenomes":[54],"with":[55],"mate":[56,61,79],"pairs.":[57],"Our":[58],"method":[59,98],"uses":[60],"pair":[62,80],"information":[63],"to":[64,75,87],"guide":[65],"contig":[66],"construction.":[67],"More":[68],"specifically,":[69],"we":[70],"developed":[71],"an":[72],"efficient":[73],"find":[76],"best":[78],"threading":[81],"paths":[82],"overlap":[85],"graph":[86],"construct":[88],"contigs.":[89],"Tests":[90],"on":[91],"simulated":[92],"data":[94],"show":[95],"that":[96],"our":[97],"produced":[99],"more":[100],"accurate":[101],"than":[103],"Celera":[104],"Assembler":[105],"and":[106],"Phrap":[107],"when":[108],"assembling":[109],"contigs":[110],"at":[111],"same":[113],"level.":[114]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
