{"id":"https://openalex.org/W2087984565","doi":"https://doi.org/10.1145/2506583.2506643","title":"Transforming Genomes Using MOD Files with Applications","display_name":"Transforming Genomes Using MOD Files with Applications","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W2087984565","doi":"https://doi.org/10.1145/2506583.2506643","mag":"2087984565"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506643","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506643","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},"type":"conference-paper","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/A5051466839","display_name":"Shun\u2010Ping Huang","orcid":"https://orcid.org/0000-0002-6060-3095"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shunping Huang","raw_affiliation_strings":["Dept. of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024296326","display_name":"Chia-Yu Kao","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chia-Yu Kao","raw_affiliation_strings":["Dept. of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042463953","display_name":"Leonard McMillan","orcid":"https://orcid.org/0000-0002-8453-0847"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leonard McMillan","raw_affiliation_strings":["Dept. of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100392089","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8180-2886"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Wang","raw_affiliation_strings":["Dept. of Computer Science, University of California, Los Angeles, CA 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":9.2274,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.97989729,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"595","last_page":"604"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.993399977684021,"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"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9904000163078308,"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/genome","display_name":"Genome","score":0.7718892097473145},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6433649659156799},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5809778571128845},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5498530864715576},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5101654529571533},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4731796085834503},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32896023988723755},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.302040159702301},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2421356439590454},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13246455788612366}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7718892097473145},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6433649659156799},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5809778571128845},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5498530864715576},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5101654529571533},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4731796085834503},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32896023988723755},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.302040159702301},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2421356439590454},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13246455788612366}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2506583.2506643","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506643","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.434.2104","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.434.2104","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.ucla.edu/~weiwang/paper/ACMBCB13_1.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1544691147","https://openalex.org/W1570564798","https://openalex.org/W1988939568","https://openalex.org/W1990061958","https://openalex.org/W1990626904","https://openalex.org/W2005501593","https://openalex.org/W2047022068","https://openalex.org/W2079236290","https://openalex.org/W2091303550","https://openalex.org/W2097065948","https://openalex.org/W2099642610","https://openalex.org/W2104190774","https://openalex.org/W2108234281","https://openalex.org/W2113312463","https://openalex.org/W2121211805","https://openalex.org/W2123497973","https://openalex.org/W2124985265","https://openalex.org/W2134199796","https://openalex.org/W2137118273","https://openalex.org/W2141458291","https://openalex.org/W2142386149","https://openalex.org/W2149992227","https://openalex.org/W2152331922","https://openalex.org/W2154442667","https://openalex.org/W2166469005","https://openalex.org/W2170551349","https://openalex.org/W2171777347","https://openalex.org/W2885727518"],"related_works":["https://openalex.org/W2921363728","https://openalex.org/W2279684808","https://openalex.org/W3137911940","https://openalex.org/W3217304749","https://openalex.org/W2894932706","https://openalex.org/W2066142713","https://openalex.org/W2767606877","https://openalex.org/W2582968398","https://openalex.org/W4223446368","https://openalex.org/W4232517363"],"abstract_inverted_index":{"Next":[0],"generation":[1],"sequencing":[2],"techniques":[3],"have":[4,49],"enabled":[5],"new":[6],"methods":[7,16],"of":[8,14,20],"DNA":[9],"and":[10,76],"RNA":[11],"quantification.":[12],"Many":[13],"these":[15],"require":[17],"a":[18],"step":[19],"aligning":[21],"short":[22],"reads":[23],"to":[24,41,52,63,67],"some":[25],"reference":[26,59],"genome.":[27],"If":[28],"the":[29,58],"target":[30],"organism":[31],"differs":[32],"significantly":[33],"from":[34],"this":[35],"reference,":[36],"alignment":[37],"errors":[38,43],"can":[39],"lead":[40],"significant":[42],"in":[44,74],"downstream":[45],"analysis.":[46],"Various":[47],"attempts":[48],"been":[50],"tried":[51],"integrate":[53],"known":[54],"genetic":[55],"variants":[56],"into":[57],"genome":[60],"so":[61],"as":[62],"construct":[64],"sample-specific":[65],"genomes":[66,79],"improve":[68],"read":[69],"alignments.":[70],"However,":[71],"many":[72],"hurdles":[73],"generating":[75],"annotating":[77],"such":[78],"remain":[80],"unsolved.":[81]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
