{"id":"https://openalex.org/W2772149630","doi":"https://doi.org/10.1109/bibm.2017.8217958","title":"An iterative algorithm for de novo optical map assembly","display_name":"An iterative algorithm for de novo optical map assembly","publication_year":2017,"publication_date":"2017-11-01","ids":{"openalex":"https://openalex.org/W2772149630","doi":"https://doi.org/10.1109/bibm.2017.8217958","mag":"2772149630"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2017.8217958","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217958","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5100747876","display_name":"Menglu Li","orcid":"https://orcid.org/0009-0008-9945-8762"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Menglu Li","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110500992","display_name":"Siu\u2010Ming Yiu","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Siu-Ming Yiu","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080235217","display_name":"Ting\u2010Fung Chan","orcid":"https://orcid.org/0000-0002-0489-3884"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ting-Fung Chan","raw_affiliation_strings":["School of Life Sciences, The Chinese University of Hong Kong, Hong Kong"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences, The Chinese University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113166810","display_name":"Ernest T. Lam","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099505","display_name":"BioNano Genomics (United States)","ror":"https://ror.org/014pv7733","country_code":"US","type":"company","lineage":["https://openalex.org/I4210099505"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ernest T. Lam","raw_affiliation_strings":["BioNano Genomics, San Diago, CA, U.S.A"],"affiliations":[{"raw_affiliation_string":"BioNano Genomics, San Diago, CA, U.S.A","institution_ids":["https://openalex.org/I4210099505"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100747876"],"corresponding_institution_ids":["https://openalex.org/I889458895"],"apc_list":null,"apc_paid":null,"fwci":0.1063,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.49860514,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"1952","last_page":"1958"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9965999722480774,"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":0.995199978351593,"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/contig","display_name":"Contig","score":0.9100189208984375},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.7914177179336548},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7150506973266602},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6395278573036194},{"id":"https://openalex.org/keywords/iterative-method","display_name":"Iterative method","score":0.6113072037696838},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.610258162021637},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5216203927993774},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.39558786153793335},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22891956567764282},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12900134921073914},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08626940846443176},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07857859134674072},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.0705035924911499}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.9100189208984375},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.7914177179336548},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7150506973266602},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6395278573036194},{"id":"https://openalex.org/C159694833","wikidata":"https://www.wikidata.org/wiki/Q2321565","display_name":"Iterative method","level":2,"score":0.6113072037696838},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.610258162021637},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5216203927993774},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.39558786153793335},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22891956567764282},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12900134921073914},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08626940846443176},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07857859134674072},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0705035924911499},{"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/bibm.2017.8217958","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217958","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1502161067","https://openalex.org/W1598134722","https://openalex.org/W1964823180","https://openalex.org/W1966822396","https://openalex.org/W1999660860","https://openalex.org/W2000597943","https://openalex.org/W2083648095","https://openalex.org/W2129933858","https://openalex.org/W2154126034","https://openalex.org/W2159960815","https://openalex.org/W2160969485","https://openalex.org/W2203319208","https://openalex.org/W2275768642","https://openalex.org/W2471897893","https://openalex.org/W2483752636","https://openalex.org/W2525022860","https://openalex.org/W2610754078","https://openalex.org/W2949860250","https://openalex.org/W6694802451"],"related_works":["https://openalex.org/W2089480001","https://openalex.org/W2885619582","https://openalex.org/W3167837387","https://openalex.org/W54719527","https://openalex.org/W4250462852","https://openalex.org/W2060480089","https://openalex.org/W2993223466","https://openalex.org/W2944010518","https://openalex.org/W2105191441","https://openalex.org/W2763602215"],"abstract_inverted_index":{"Optical":[0],"mapping":[1],"is":[2],"a":[3,36,92,108],"high-throughput":[4],"sequencing":[5],"technology":[6],"which":[7],"carries":[8],"long-range":[9],"genome":[10,33],"information":[11],"at":[12],"no":[13],"risk":[14,38],"of":[15,20,39,87,95],"PCR":[16],"artifacts.":[17],"On":[18],"account":[19],"its":[21],"long":[22],"span,":[23],"optical":[24,46,58,116],"maps":[25],"leave":[26],"much":[27],"fewer":[28],"gaps":[29],"when":[30],"used":[31,72,124],"for":[32,55,83],"assembly.":[34,48,60,88,98],"However,":[35],"high":[37],"errors":[40],"poses":[41],"an":[42,52],"enormous":[43],"challenge":[44],"to":[45,73],"map":[47,59,117],"Here":[49],"we":[50],"propose":[51],"iterative":[53,100],"algorithm":[54],"de":[56],"novo":[57],"In":[61,111],"any":[62],"iteration,":[63],"only":[64],"significant":[65],"pairwise":[66],"alignments":[67],"beyond":[68],"strict":[69],"thresholds":[70,90],"are":[71],"construct":[74],"accurate":[75],"contigs.":[76],"These":[77],"contigs":[78,106],"act":[79],"as":[80],"input":[81],"molecules":[82],"the":[84,96,103,126],"next":[85],"iteration":[86],"Strict":[89],"ensures":[91],"good":[93],"quality":[94],"local":[97],"The":[99],"method":[101],"retains":[102],"connectivity":[104],"between":[105],"in":[107,125],"progressive":[109],"manner.":[110],"practice,":[112],"our":[113],"IOMA":[114],"(iterative":[115],"assembler)":[118],"outperforms":[119],"two":[120],"popular":[121],"assemblers":[122],"being":[123],"community":[127],"on":[128],"both":[129],"simulated":[130],"and":[131],"real":[132],"E.":[133],"coli":[134],"datasets.":[135]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
