{"id":"https://openalex.org/W2114133992","doi":"https://doi.org/10.1093/bib/bbp026","title":"Genome assembly reborn: recent computational challenges","display_name":"Genome assembly reborn: recent computational challenges","publication_year":2009,"publication_date":"2009-05-29","ids":{"openalex":"https://openalex.org/W2114133992","doi":"https://doi.org/10.1093/bib/bbp026","mag":"2114133992","pmid":"https://pubmed.ncbi.nlm.nih.gov/19482960"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbp026","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbp026","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2691937","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064979917","display_name":"Mihai Pop","orcid":"https://orcid.org/0000-0001-9617-5304"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M. Pop","raw_affiliation_strings":["Department of Computer Science and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park, MD 20742, USA. mpop@umd.edu","Department of Computer Science and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park, MD 20742, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park, MD 20742, USA. mpop@umd.edu","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Department of Computer Science and the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park, MD 20742, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064979917"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":14.9241,"has_fulltext":false,"cited_by_count":388,"citation_normalized_percentile":{"value":0.99431201,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"10","issue":"4","first_page":"354","last_page":"366"},"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9797999858856201,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.974399983882904,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7599881291389465},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6542820930480957},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.6467729210853577},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.6240828037261963},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5235847234725952},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.507030725479126},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.4763355851173401},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.44867655634880066},{"id":"https://openalex.org/keywords/personal-genomics","display_name":"Personal genomics","score":0.4386309087276459},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.43030446767807007},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41866278648376465},{"id":"https://openalex.org/keywords/cancer-genome-sequencing","display_name":"Cancer genome sequencing","score":0.4184894263744354},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3885040581226349},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2027776837348938},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15334674715995789}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7599881291389465},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6542820930480957},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6467729210853577},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.6240828037261963},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5235847234725952},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.507030725479126},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4763355851173401},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.44867655634880066},{"id":"https://openalex.org/C24103923","wikidata":"https://www.wikidata.org/wiki/Q7170583","display_name":"Personal genomics","level":5,"score":0.4386309087276459},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.43030446767807007},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41866278648376465},{"id":"https://openalex.org/C205270622","wikidata":"https://www.wikidata.org/wiki/Q17082639","display_name":"Cancer genome sequencing","level":5,"score":0.4184894263744354},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3885040581226349},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2027776837348938},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15334674715995789},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"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},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbp026","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbp026","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:19482960","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19482960","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},{"id":"pmh:oai:pubmedcentral.nih.gov:2691937","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2691937","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:2691937","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2691937","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5699999928474426}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":75,"referenced_works":["https://openalex.org/W62450904","https://openalex.org/W1521760908","https://openalex.org/W1635391495","https://openalex.org/W1841715584","https://openalex.org/W1850079471","https://openalex.org/W1897166569","https://openalex.org/W1963524639","https://openalex.org/W1966711026","https://openalex.org/W1966822396","https://openalex.org/W1970939265","https://openalex.org/W1974646727","https://openalex.org/W1975736716","https://openalex.org/W1986098362","https://openalex.org/W1992950355","https://openalex.org/W2001725958","https://openalex.org/W2008235493","https://openalex.org/W2016848076","https://openalex.org/W2020053713","https://openalex.org/W2021284638","https://openalex.org/W2022910024","https://openalex.org/W2023911006","https://openalex.org/W2029139020","https://openalex.org/W2033531015","https://openalex.org/W2034225042","https://openalex.org/W2042008515","https://openalex.org/W2043714862","https://openalex.org/W2058370375","https://openalex.org/W2060384505","https://openalex.org/W2090705041","https://openalex.org/W2093830129","https://openalex.org/W2095948526","https://openalex.org/W2097529842","https://openalex.org/W2099570444","https://openalex.org/W2100237209","https://openalex.org/W2101021876","https://openalex.org/W2106097547","https://openalex.org/W2112113834","https://openalex.org/W2113601822","https://openalex.org/W2113649367","https://openalex.org/W2114344422","https://openalex.org/W2114765236","https://openalex.org/W2119923823","https://openalex.org/W2120414630","https://openalex.org/W2121016876","https://openalex.org/W2124637227","https://openalex.org/W2127230663","https://openalex.org/W2127651281","https://openalex.org/W2128114769","https://openalex.org/W2129220104","https://openalex.org/W2129795133","https://openalex.org/W2131852975","https://openalex.org/W2132415967","https://openalex.org/W2136651963","https://openalex.org/W2137509018","https://openalex.org/W2138270253","https://openalex.org/W2141324508","https://openalex.org/W2142642738","https://openalex.org/W2142749416","https://openalex.org/W2144662851","https://openalex.org/W2145336165","https://openalex.org/W2151017710","https://openalex.org/W2154431984","https://openalex.org/W2154915161","https://openalex.org/W2155845142","https://openalex.org/W2156095709","https://openalex.org/W2156104322","https://openalex.org/W2159998739","https://openalex.org/W2160969485","https://openalex.org/W2164075646","https://openalex.org/W2164631357","https://openalex.org/W2166265186","https://openalex.org/W2171531867","https://openalex.org/W2292905290","https://openalex.org/W2616754551","https://openalex.org/W2912500497"],"related_works":["https://openalex.org/W4324130370","https://openalex.org/W4254892634","https://openalex.org/W2734838959","https://openalex.org/W4322485252","https://openalex.org/W1978155433","https://openalex.org/W2522810657","https://openalex.org/W2482749883","https://openalex.org/W2041379552","https://openalex.org/W2903885984","https://openalex.org/W173031013"],"abstract_inverted_index":{"Research":[0],"into":[1],"genome":[2,23,105],"assembly":[3,106],"algorithms":[4],"has":[5,60],"experienced":[6],"a":[7],"resurgence":[8],"due":[9],"to":[10,44,62,91],"new":[11,35,69,74,92],"challenges":[12],"created":[13],"by":[14],"the":[15,34,39,45,52,73,100],"development":[16],"of":[17,55,66,76,82,87],"next":[18,56],"generation":[19,57],"sequencing":[20,58,67,81],"technologies.":[21],"Several":[22],"assemblers":[24],"have":[25],"been":[26],"published":[27],"in":[28,68,111],"recent":[29,109],"years":[30],"specifically":[31],"targeted":[32],"at":[33],"sequence":[36],"data;":[37],"however,":[38],"ever-changing":[40],"technological":[41],"landscape":[42],"leads":[43],"need":[46],"for":[47,104],"continued":[48],"research.":[49],"In":[50,95],"addition,":[51],"low":[53],"cost":[54],"data":[59],"led":[61],"an":[63],"increased":[64],"use":[65],"settings.":[70],"For":[71],"example,":[72],"field":[75],"metagenomics":[77],"relies":[78],"on":[79],"large-scale":[80],"entire":[83],"microbial":[84],"communities":[85],"instead":[86],"isolate":[88],"genomes,":[89],"leading":[90],"computational":[93],"challenges.":[94],"this":[96,112],"article,":[97],"we":[98],"outline":[99],"major":[101],"algorithmic":[102],"approaches":[103],"and":[107],"describe":[108],"developments":[110],"domain.":[113]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":24},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":23},{"year":2017,"cited_by_count":21},{"year":2016,"cited_by_count":23},{"year":2015,"cited_by_count":28},{"year":2014,"cited_by_count":41},{"year":2013,"cited_by_count":50},{"year":2012,"cited_by_count":45}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
