{"id":"https://openalex.org/W2126748131","doi":"https://doi.org/10.1109/csb.2003.1227330","title":"A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression vectors","display_name":"A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression vectors","publication_year":2004,"publication_date":"2004-03-30","ids":{"openalex":"https://openalex.org/W2126748131","doi":"https://doi.org/10.1109/csb.2003.1227330","mag":"2126748131","pmid":"https://pubmed.ncbi.nlm.nih.gov/16452805"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227330","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227330","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://stars.library.ucf.edu/scopus2000/1932","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077012914","display_name":"Ravi Vijaya Satya","orcid":null},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ravi Vijaya Satya","raw_affiliation_strings":["School of Engineering and Computer Science, University of Central Florida, Orlando, FL, USA"],"affiliations":[{"raw_affiliation_string":"School of Engineering and Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109107792","display_name":"Amar Mukherjee","orcid":"https://orcid.org/0009-0003-7658-6132"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amar Mukherjee","raw_affiliation_strings":["School of Engineering and Computer Science, University of Central Florida, Orlando, FL, USA"],"affiliations":[{"raw_affiliation_string":"School of Engineering and Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020997464","display_name":"Udaykumar Ranga","orcid":"https://orcid.org/0000-0003-3726-7932"},"institutions":[{"id":"https://openalex.org/I147481903","display_name":"Jawaharlal Nehru Centre for Advanced Scientific Research","ror":"https://ror.org/0538gdx71","country_code":"IN","type":"facility","lineage":["https://openalex.org/I147481903","https://openalex.org/I2799351866","https://openalex.org/I4210098748","https://openalex.org/I4210134808"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Udaykumar Ranga","raw_affiliation_strings":["Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India"],"affiliations":[{"raw_affiliation_string":"Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India","institution_ids":["https://openalex.org/I147481903"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5077012914"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":null,"apc_paid":null,"fwci":0.6029,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.65836776,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"72","issue":null,"first_page":"294","last_page":"305"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10725","display_name":"RNA Interference and Gene Delivery","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/T10725","display_name":"RNA Interference and Gene Delivery","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cpg-site","display_name":"CpG site","score":0.5511863827705383},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5255540609359741},{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.4802265763282776},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4778808653354645},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4442063868045807},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4125223159790039},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3674810826778412},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3650580644607544},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.34366005659103394},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.285788357257843},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.23161152005195618},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.20128357410430908},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.1645326018333435}],"concepts":[{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.5511863827705383},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5255540609359741},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.4802265763282776},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4778808653354645},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4442063868045807},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4125223159790039},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3674810826778412},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3650580644607544},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.34366005659103394},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.285788357257843},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.23161152005195618},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.20128357410430908},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.1645326018333435}],"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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005818","descriptor_name":"Genetic Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005822","descriptor_name":"Genetic Vectors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005822","descriptor_name":"Genetic Vectors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005822","descriptor_name":"Genetic Vectors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019444","descriptor_name":"Vaccines, DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019444","descriptor_name":"Vaccines, DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019444","descriptor_name":"Vaccines, DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1109/csb.2003.1227330","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227330","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},{"id":"pmid:16452805","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16452805","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":"Proceedings. IEEE Computer Society Bioinformatics Conference","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.103.1307","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.1307","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://conferences.computer.org/bioinformatics/CSB2003/PDF/reg_pprs/029-satya.pdf","raw_type":"text"},{"id":"pmh:oai:stars.library.ucf.edu:scopus2000-2931","is_oa":true,"landing_page_url":"https://stars.library.ucf.edu/scopus2000/1932","pdf_url":null,"source":{"id":"https://openalex.org/S4210172555","display_name":"Journal of International Crisis and Risk Communication Research","issn_l":"2576-0017","issn":["2576-0017","2576-0025"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus Export 2000s","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:stars.library.ucf.edu:scopus2000-2931","is_oa":true,"landing_page_url":"https://stars.library.ucf.edu/scopus2000/1932","pdf_url":null,"source":{"id":"https://openalex.org/S4210172555","display_name":"Journal of International Crisis and Risk Communication Research","issn_l":"2576-0017","issn":["2576-0017","2576-0025"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus Export 2000s","raw_type":"text"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.5899999737739563}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W180692248","https://openalex.org/W938539187","https://openalex.org/W1481002459","https://openalex.org/W1537788154","https://openalex.org/W1964770087","https://openalex.org/W1970708694","https://openalex.org/W1971592398","https://openalex.org/W1971604280","https://openalex.org/W1977550154","https://openalex.org/W1981747163","https://openalex.org/W1990061958","https://openalex.org/W2010608533","https://openalex.org/W2014495927","https://openalex.org/W2016817833","https://openalex.org/W2016862474","https://openalex.org/W2020812527","https://openalex.org/W2035634951","https://openalex.org/W2039420133","https://openalex.org/W2043572676","https://openalex.org/W2046027100","https://openalex.org/W2060593488","https://openalex.org/W2061009669","https://openalex.org/W2062371771","https://openalex.org/W2067041330","https://openalex.org/W2087395692","https://openalex.org/W2099964107","https://openalex.org/W2106014927","https://openalex.org/W2108961890","https://openalex.org/W2109352986","https://openalex.org/W2111726077","https://openalex.org/W2115992869","https://openalex.org/W2118011548","https://openalex.org/W2129166390","https://openalex.org/W2132568167","https://openalex.org/W2135073267","https://openalex.org/W2140008985","https://openalex.org/W2141028568","https://openalex.org/W2154653263","https://openalex.org/W2158798674","https://openalex.org/W2164618276","https://openalex.org/W2319994857","https://openalex.org/W2610179052","https://openalex.org/W6684041852"],"related_works":["https://openalex.org/W1531710418","https://openalex.org/W2355920812","https://openalex.org/W1979257839","https://openalex.org/W2189061370","https://openalex.org/W1972740636","https://openalex.org/W2088156872","https://openalex.org/W2910946914","https://openalex.org/W2129444033","https://openalex.org/W2094816155","https://openalex.org/W2981250203"],"abstract_inverted_index":{"Codon":[0],"optimization":[1],"enhances":[2],"the":[3,50,65,68,71,75,107,131,134],"efficiency":[4],"of":[5,46,70,133],"DNA":[6,11,51,76,92],"expression":[7,52,77],"vectors":[8,53],"used":[9],"in":[10,49,74,111],"vaccination":[12],"and":[13,61,67,100],"gene":[14],"therapy":[15],"by":[16],"increasing":[17],"protein":[18],"expression.":[19],"Additionally,":[20],"certain":[21,32,120],"nucleotide":[22],"motifs":[23,48,73],"have":[24],"experimentally":[25],"been":[26],"shown":[27],"to":[28,41,55,83,89],"be":[29],"immuno-stimulatory":[30],"while":[31],"others":[33],"immuno-suppressive.":[34],"In":[35],"this":[36],"paper,":[37],"we":[38,141],"present":[39],"algorithms":[40,88],"locate":[42],"a":[43,56,91,95,101,112,143],"given":[44,57,96],"set":[45],"immuno-modulatory":[47,72],"corresponding":[54],"amino":[58,97,135],"acid":[59,98,136],"sequence":[60,93,99],"maximize":[62,117],"or":[63,118],"minimize":[64,119],"number":[66],"context":[69],"vectors.":[78],"The":[79],"main":[80],"contribution":[81],"is":[82,123,130],"use":[84],"multiple":[85],"pattern":[86],"matching":[87],"synthesize":[90],"for":[94,105],"graph":[102,114],"theoretic":[103],"approach":[104],"finding":[106],"longest":[108],"weighted":[109],"path":[110],"directed":[113],"that":[115],"will":[116],"motifs.":[121],"This":[122],"achieved":[124],"using":[125],"O(n(2))":[126],"time,":[127],"where":[128],"n":[129],"length":[132],"sequence.":[137],"Based":[138],"on":[139],"this,":[140],"develop":[142],"software":[144],"tool.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}