{"id":"https://openalex.org/W2675631482","doi":"https://doi.org/10.1093/bib/bby003","title":"Modeling biological problems in computer science: a case study in genome assembly","display_name":"Modeling biological problems in computer science: a case study in genome assembly","publication_year":2018,"publication_date":"2018-01-09","ids":{"openalex":"https://openalex.org/W2675631482","doi":"https://doi.org/10.1093/bib/bby003","mag":"2675631482","pmid":"https://pubmed.ncbi.nlm.nih.gov/29394324"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby003","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby003","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":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1706.05429","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066909672","display_name":"Paul Medvedev","orcid":"https://orcid.org/0000-0003-3143-594X"},"institutions":[{"id":"https://openalex.org/I4210100303","display_name":"Biotech Park","ror":"https://ror.org/00mv0vt78","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210100303"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Paul Medvedev","raw_affiliation_strings":["Corresponding author. Paul Medvedev, Department of Computer Science and Engineering, Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, 506B Wartik Lab, University Park, PA 16802, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Corresponding author. Paul Medvedev, Department of Computer Science and Engineering, Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, 506B Wartik Lab, University Park, PA 16802, USA","institution_ids":["https://openalex.org/I4210100303"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066909672"],"corresponding_institution_ids":["https://openalex.org/I4210100303"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.165,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.46625826,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"4","first_page":"1376","last_page":"1383"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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":0.9988999962806702,"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":0.9926000237464905,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9854999780654907,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant 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/realm","display_name":"Realm","score":0.9021139144897461},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6271464824676514},{"id":"https://openalex.org/keywords/face","display_name":"Face (sociological concept)","score":0.5530295968055725},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5320906043052673},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.45820310711860657},{"id":"https://openalex.org/keywords/genome-editing","display_name":"Genome editing","score":0.4380645751953125},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.42258119583129883},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37460190057754517},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17177391052246094},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1252327561378479},{"id":"https://openalex.org/keywords/sociology","display_name":"Sociology","score":0.11549010872840881},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09306582808494568},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07653495669364929}],"concepts":[{"id":"https://openalex.org/C2778757428","wikidata":"https://www.wikidata.org/wiki/Q1250464","display_name":"Realm","level":2,"score":0.9021139144897461},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6271464824676514},{"id":"https://openalex.org/C2779304628","wikidata":"https://www.wikidata.org/wiki/Q3503480","display_name":"Face (sociological concept)","level":2,"score":0.5530295968055725},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5320906043052673},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.45820310711860657},{"id":"https://openalex.org/C144501496","wikidata":"https://www.wikidata.org/wiki/Q5533489","display_name":"Genome editing","level":4,"score":0.4380645751953125},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.42258119583129883},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37460190057754517},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17177391052246094},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1252327561378479},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.11549010872840881},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09306582808494568},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07653495669364929},{"id":"https://openalex.org/C36289849","wikidata":"https://www.wikidata.org/wiki/Q34749","display_name":"Social science","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"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":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bby003","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby003","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:29394324","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29394324","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:arXiv.org:1706.05429","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1706.05429","pdf_url":"https://arxiv.org/pdf/1706.05429","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:2675631482","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1706.05429","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1706.05429","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1706.05429","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1706.05429","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1706.05429","pdf_url":"https://arxiv.org/pdf/1706.05429","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.5899999737739563,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G6472907709","display_name":null,"funder_award_id":"1421908","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"},{"id":"https://openalex.org/G667564425","display_name":null,"funder_award_id":"1453527","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"},{"id":"https://openalex.org/G6723414785","display_name":null,"funder_award_id":"1439057","funder_id":"https://openalex.org/F4320337387","funder_display_name":"Division of Computing and Communication Foundations"},{"id":"https://openalex.org/G7827526042","display_name":null,"funder_award_id":"1356529","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"}],"funders":[{"id":"https://openalex.org/F4320337387","display_name":"Division of Computing and Communication Foundations","ror":"https://ror.org/01mng8331"},{"id":"https://openalex.org/F4320337389","display_name":"Division of Information and Intelligent Systems","ror":"https://ror.org/053a2cp42"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2675631482.pdf","grobid_xml":"https://content.openalex.org/works/W2675631482.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1972924519","https://openalex.org/W2001792012","https://openalex.org/W2105067980","https://openalex.org/W2108640362","https://openalex.org/W2152073175","https://openalex.org/W2157624015","https://openalex.org/W2537565528"],"related_works":["https://openalex.org/W2962686126","https://openalex.org/W2403250674","https://openalex.org/W2294236252","https://openalex.org/W2075599722","https://openalex.org/W2407858905","https://openalex.org/W2267638272","https://openalex.org/W2735085336","https://openalex.org/W1635873948","https://openalex.org/W1940281766","https://openalex.org/W3021782748","https://openalex.org/W2291904938","https://openalex.org/W1618105221","https://openalex.org/W2552749884","https://openalex.org/W2120158030","https://openalex.org/W2912784069","https://openalex.org/W28481040","https://openalex.org/W2914857323","https://openalex.org/W2198488435","https://openalex.org/W2206943345","https://openalex.org/W2980109914"],"abstract_inverted_index":{"As":[0],"computer":[1,64],"scientists":[2],"working":[3],"in":[4,25,55,62],"bioinformatics/computational":[5],"biology,":[6],"we":[7,38],"often":[8],"face":[9],"the":[10,40,43,56,63,69,75],"challenge":[11],"of":[12,42],"coming":[13],"up":[14],"with":[15],"an":[16,84],"algorithm":[17],"to":[18,47,50,59,86],"answer":[19],"a":[20,53,60],"biological":[21,57],"question.":[22],"This":[23],"occurs":[24],"many":[26],"areas,":[27],"such":[28],"as":[29,95],"variant":[30],"calling,":[31],"alignment":[32],"and":[33,100],"assembly.":[34],"In":[35],"this":[36,81],"tutorial,":[37],"use":[39],"example":[41],"genome":[44,88],"assembly":[45,89],"problem":[46],"demonstrate":[48],"how":[49,87],"go":[51],"from":[52],"question":[54],"realm":[58],"solution":[61],"science":[65],"realm.":[66],"We":[67],"show":[68],"modeling":[70],"process":[71],"step-by-step,":[72],"including":[73],"all":[74],"intermediate":[76],"failed":[77],"attempts.":[78],"Please":[79],"note":[80],"is":[82],"not":[83],"introduction":[85],"algorithms":[90],"work":[91],"and,":[92],"if":[93],"treated":[94],"such,":[96],"would":[97],"be":[98],"incomplete":[99],"unnecessarily":[101],"long-winded.":[102]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2022-10-03T00:00:00"}
