{"id":"https://openalex.org/W2133874274","doi":"https://doi.org/10.1109/bibm.2012.6392622","title":"MDAsim: A multiple displacement amplification simulator","display_name":"MDAsim: A multiple displacement amplification simulator","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W2133874274","doi":"https://doi.org/10.1109/bibm.2012.6392622","mag":"2133874274"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2012.6392622","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"proceedings-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/A5014953247","display_name":"Zeinab Tagliavi","orcid":null},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zeinab Tagliavi","raw_affiliation_strings":["Dept. of Computer Science, Wayne State University, Detroit, MI 48202."],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Wayne State University, Detroit, MI 48202.","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006190733","display_name":"Sorin Dr\u0103ghici","orcid":"https://orcid.org/0000-0002-0786-8377"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sorin Draghici","raw_affiliation_strings":["Department of Clinical and Translational Science, Department of Computer Science, Wayne State University, Detroit, MI 48202"],"affiliations":[{"raw_affiliation_string":"Department of Clinical and Translational Science, Department of Computer Science, Wayne State University, Detroit, MI 48202","institution_ids":["https://openalex.org/I185443292"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.592,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":10,"citation_normalized_percentile":{"value":0.908235,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":85,"max":86},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"RNA Sequencing Data Analysis","score":0.9954,"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":"RNA Sequencing Data Analysis","score":0.9954,"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/T11289","display_name":"Comprehensive Integration of Single-Cell Transcriptomic Data","score":0.9876,"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/T11287","display_name":"Genomic Landscape of Cancer and Mutational Signatures","score":0.9742,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/amplicon","display_name":"Amplicon","score":0.76064163},{"id":"https://openalex.org/keywords/multiple-displacement-amplification","display_name":"Multiple displacement amplification","score":0.71448255},{"id":"https://openalex.org/keywords/metagenomics-assembly","display_name":"metagenomics assembly","score":0.509268}],"concepts":[{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.76064163},{"id":"https://openalex.org/C156385826","wikidata":"https://www.wikidata.org/wiki/Q1341059","display_name":"Multiple displacement amplification","level":5,"score":0.71448255},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6419394},{"id":"https://openalex.org/C60635243","wikidata":"https://www.wikidata.org/wiki/Q6675780","display_name":"Loop-mediated isothermal amplification","level":3,"score":0.5582308},{"id":"https://openalex.org/C107551265","wikidata":"https://www.wikidata.org/wiki/Q1458245","display_name":"Displacement (psychology)","level":2,"score":0.5552294},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4519243},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3989053},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.39395732},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.36731505},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.34481975},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34073108},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.27326444},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20641842},{"id":"https://openalex.org/C78063203","wikidata":"https://www.wikidata.org/wiki/Q3062596","display_name":"DNA extraction","level":4,"score":0.15189251},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12974876},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09468198},{"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/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2012.6392622","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":null,"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":5,"referenced_works":["https://openalex.org/W1968762427","https://openalex.org/W2086814185","https://openalex.org/W2103441770","https://openalex.org/W2113287691","https://openalex.org/W2157539385"],"related_works":["https://openalex.org/W4307003200","https://openalex.org/W4225401919","https://openalex.org/W3128052307","https://openalex.org/W2790795989","https://openalex.org/W2499234632","https://openalex.org/W2338809804","https://openalex.org/W2165332294","https://openalex.org/W2069913772","https://openalex.org/W2065098811","https://openalex.org/W1979974453"],"abstract_inverted_index":{"Multiple":[0],"displacement":[1],"amplification":[2,11,58,72],"(MDA)":[3],"is":[4,30,59,64],"a":[5,22,81,91,104,135],"fast":[6],"non-PCR":[7],"based":[8],"isothermal":[9],"DNA":[10,19],"method":[12],"that":[13,69,117,158],"can":[14,138,181],"amplify":[15],"small":[16],"amounts":[17],"of":[18,44,47,84,121,132,145,152,165],"samples":[20],"to":[21,102,184],"reasonable":[23],"quantity":[24],"for":[25,32,51,107,141],"genomic":[26],"analysis.":[27],"This":[28,62],"technique":[29],"suitable":[31],"metagenomics":[33],"and":[34,39,66,95,134,143,163],"single":[35,52,146],"cell":[36,53,147],"genome":[37],"sequencing":[38,136],"related":[40],"analyses.":[41],"The":[42],"distribution":[43,63],"the":[45,48,56,67,85,96,108,118,124,130,150,160,175],"coverage":[46,120,126],"output":[49,109,119],"amplicons":[50],"MDA":[54,86,161,176,188],"unlike":[55],"multiceli":[57],"not":[60,75],"uniform.":[61],"unknown,":[65],"parameters":[68],"affect":[70],"this":[71,112],"bias":[73],"have":[74,80,89],"been":[76],"studied":[77],"thoroughly.":[78],"To":[79],"better":[82],"understanding":[83],"reaction":[87],"we":[88,114],"developed":[90],"simplified":[92],"mathematical":[93],"model":[94,106],"corresponding":[97],"simulation":[98,164],"algorithm":[99],"called":[100],"MDAsim":[101,122,133],"obtain":[103],"generative":[105],"amplicons.":[110],"In":[111],"paper":[113],"will":[115],"show":[116],"matches":[123],"experimental":[125,153],"very":[127],"well.":[128],"Therefore,":[129],"combination":[131],"simulator":[137],"be":[139,182],"utilized":[140],"test":[142],"evaluation":[144],"assemblers":[148],"avoiding":[149],"burden":[151],"sequencing.":[154],"Our":[155],"results":[156],"suggest":[157],"modelling":[159],"mechanism":[162],"such":[166],"increasingly":[167],"complex":[168],"models":[169],"may":[170],"provide":[171],"valuable":[172],"insight":[173],"into":[174],"process,":[177],"which":[178],"in":[179],"turn":[180],"used":[183],"design":[185],"more":[186],"efficient":[187],"reactions.":[189]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2133874274","counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2024-09-27T00:08:32.594063","created_date":"2016-06-24"}
