{"id":"https://openalex.org/W2034054625","doi":"https://doi.org/10.1089/cmb.2011.0201","title":"Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads","display_name":"Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads","publication_year":2011,"publication_date":"2011-12-16","ids":{"openalex":"https://openalex.org/W2034054625","doi":"https://doi.org/10.1089/cmb.2011.0201","mag":"2034054625","pmid":"https://pubmed.ncbi.nlm.nih.gov/22175250"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2011.0201","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2011.0201","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1089/cmb.2011.0201","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066700750","display_name":"P. Carnevali","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Paolo Carnevali","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California 94043, USA"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California 94043, USA","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076674835","display_name":"Jonathan Baccash","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Baccash","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111911477","display_name":"Aaron L. Halpern","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron L. Halpern","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087102153","display_name":"Igor Nazarenko","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Igor Nazarenko","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044237086","display_name":"Geoffrey B. Nilsen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Geoffrey B. Nilsen","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043579276","display_name":"Krishna Prasad Pant","orcid":"https://orcid.org/0000-0002-2668-2607"},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Krishna P. Pant","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073678594","display_name":"Jessica Ebert","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jessica C. Ebert","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002527404","display_name":"Anushka Brownley","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anushka Brownley","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025848610","display_name":"Matt Morenzoni","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matt Morenzoni","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031391290","display_name":"Vitali Karpinchyk","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vitali Karpinchyk","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042203689","display_name":"Bruce Martin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruce Martin","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056317654","display_name":"Dennis G. Ballinger","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dennis G. Ballinger","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062532960","display_name":"Radoje Drmanac","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087390","display_name":"Complete Genomics (United States)","ror":"https://ror.org/0046r4y62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210087390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Radoje Drmanac","raw_affiliation_strings":["Complete Genomics Inc","Complete Genomics Inc., Mountain View, California"],"affiliations":[{"raw_affiliation_string":"Complete Genomics Inc","institution_ids":["https://openalex.org/I4210087390"]},{"raw_affiliation_string":"Complete Genomics Inc., Mountain View, California","institution_ids":["https://openalex.org/I4210087390"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5066700750"],"corresponding_institution_ids":["https://openalex.org/I4210087390"],"apc_list":null,"apc_paid":null,"fwci":3.0578,"has_fulltext":false,"cited_by_count":95,"citation_normalized_percentile":{"value":0.91934811,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"19","issue":"3","first_page":"279","last_page":"292"},"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":0.996399998664856,"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":0.9962999820709229,"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/computer-science","display_name":"Computer science","score":0.6093716025352478},{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.5913213491439819},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5223625898361206},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5135962963104248},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.47549188137054443},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.45820072293281555},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.45804163813591003},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43563351035118103},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.42199188470840454},{"id":"https://openalex.org/keywords/local-optimum","display_name":"Local optimum","score":0.41974204778671265},{"id":"https://openalex.org/keywords/shuffling","display_name":"Shuffling","score":0.4122299551963806},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3276416063308716},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24220529198646545},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20136284828186035},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18130862712860107},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14709129929542542},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.11522862315177917}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6093716025352478},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.5913213491439819},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5223625898361206},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5135962963104248},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.47549188137054443},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.45820072293281555},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.45804163813591003},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43563351035118103},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.42199188470840454},{"id":"https://openalex.org/C141934464","wikidata":"https://www.wikidata.org/wiki/Q3305386","display_name":"Local optimum","level":2,"score":0.41974204778671265},{"id":"https://openalex.org/C167927819","wikidata":"https://www.wikidata.org/wiki/Q1930567","display_name":"Shuffling","level":2,"score":0.4122299551963806},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3276416063308716},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24220529198646545},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20136284828186035},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18130862712860107},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14709129929542542},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.11522862315177917},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0},{"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/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1089/cmb.2011.0201","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2011.0201","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:22175250","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22175250","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 computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":{"id":"doi:10.1089/cmb.2011.0201","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2011.0201","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1528782506","https://openalex.org/W1973950074","https://openalex.org/W2000905326","https://openalex.org/W2001725958","https://openalex.org/W2012016911","https://openalex.org/W2021284638","https://openalex.org/W2037953066","https://openalex.org/W2087297876","https://openalex.org/W2093931624","https://openalex.org/W2100745860","https://openalex.org/W2108487922","https://openalex.org/W2112113834","https://openalex.org/W2112228737","https://openalex.org/W2118246164","https://openalex.org/W2119180969","https://openalex.org/W2121016876","https://openalex.org/W2134653489","https://openalex.org/W2136651963","https://openalex.org/W2138603354","https://openalex.org/W2153010521","https://openalex.org/W2168133698","https://openalex.org/W2168142506","https://openalex.org/W2171777347","https://openalex.org/W2885727518"],"related_works":["https://openalex.org/W1820394219","https://openalex.org/W220770808","https://openalex.org/W4283384467","https://openalex.org/W3121387483","https://openalex.org/W2767590279","https://openalex.org/W3090794301","https://openalex.org/W2772185703","https://openalex.org/W4302591804","https://openalex.org/W2173935179","https://openalex.org/W2213265806"],"abstract_inverted_index":{"Unchained":[0],"base":[1],"reads":[2],"on":[3,40,155],"self-assembling":[4],"DNA":[5],"nanoarrays":[6],"have":[7],"recently":[8],"emerged":[9],"as":[10,37],"a":[11,93,112,178],"promising":[12],"approach":[13],"to":[14,72,90,140,161,168,174,183],"low-cost,":[15],"high-quality":[16],"resequencing":[17,34],"of":[18,22,25,59,74,172,193],"human":[19],"genomes.":[20],"Because":[21],"unique":[23],"characteristics":[24],"these":[26],"mated":[27],"pair":[28],"reads,":[29],"existing":[30],"computational":[31,53],"methods":[32,54,70],"for":[33,46,56],"assembly,":[35],"such":[36],"those":[38],"based":[39,154],"map-consensus":[41],"calling,":[42],"are":[43],"not":[44],"adequate":[45],"accurate":[47,57],"variant":[48],"calling.":[49],"We":[50,79],"describe":[51],"novel":[52],"developed":[55],"calling":[58],"SNPs":[60],"and":[61,64,117,134],"short":[62],"substitutions":[63],"indels":[65],"(<100":[66],"bp);":[67],"the":[68,87,97,122,163,170,185,191,197],"same":[69],"apply":[71],"evaluation":[73],"hypothesized":[75],"larger,":[76],"structural":[77],"variations.":[78],"use":[80],"an":[81,141],"optimization":[82,127,164],"process":[83,128,165],"that":[84,120,151],"iteratively":[85,129],"adjusts":[86],"genome":[88],"sequence":[89],"maximize":[91],"its":[92],"posteriori":[94],"probability":[95,105],"given":[96],"observed":[98],"reads.":[99],"For":[100],"each":[101],"candidate":[102],"sequence,":[103],"this":[104],"is":[106,138,159,181],"computed":[107],"using":[108],"Bayesian":[109],"statistics":[110],"with":[111],"simple":[113],"read":[114],"generation":[115],"model":[116],"simplifying":[118],"assumptions":[119],"make":[121],"problem":[123],"computationally":[124],"tractable.":[125],"The":[126],"applies":[130],"one-base":[131],"substitutions,":[132],"insertions,":[133],"deletions":[135],"until":[136],"convergence":[137],"achieved":[139],"optimum":[142],"diploid":[143],"sequence.":[144],"A":[145],"local":[146,175],"de":[147],"novo":[148],"assembly":[149],"procedure":[150],"generalizes":[152],"approaches":[153],"De":[156],"Bruijn":[157],"graphs":[158],"used":[160],"seed":[162],"in":[166,196],"order":[167],"reduce":[169,184],"chance":[171],"converging":[173],"optima.":[176],"Finally,":[177],"correlation-based":[179],"filter":[180],"applied":[182],"false":[186],"positive":[187],"rate":[188],"caused":[189],"by":[190],"presence":[192],"repetitive":[194],"regions":[195],"reference":[198],"genome.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":18},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":5}],"updated_date":"2026-03-13T14:20:09.374765","created_date":"2025-10-10T00:00:00"}
