{"id":"https://openalex.org/W2167862746","doi":"https://doi.org/10.1109/tcbb.2004.12","title":"Sequencing-by-hybridization revisited: the analog-spectrum proposal","display_name":"Sequencing-by-hybridization revisited: the analog-spectrum proposal","publication_year":2004,"publication_date":"2004-01-01","ids":{"openalex":"https://openalex.org/W2167862746","doi":"https://doi.org/10.1109/tcbb.2004.12","mag":"2167862746","pmid":"https://pubmed.ncbi.nlm.nih.gov/17048407"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2004.12","doi":"https://doi.org/10.1109/tcbb.2004.12","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2004.12","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","dongbi-b","doyens","jufo-2","medline","norway-1","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"parent_works":[],"lineage":["https://openalex.org/W2167862746"],"child_works_count":0,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"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/A5112003802","display_name":"F. P. Preparata","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"F.P. Preparata","raw_affiliation_strings":["Computer Science Department, Brown University, 115 Waterman Street, Providence, RI 02912-1910, USA. franco@cs.brown.edu","Computer Science Department, Brown University, Providence, RI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Brown University, 115 Waterman Street, Providence, RI 02912-1910, USA. franco@cs.brown.edu","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Computer Science Department, Brown University, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5112003802"],"corresponding_institution_ids":["https://openalex.org/I27804330"],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":17.8149,"has_fulltext":false,"cited_by_count":319,"citation_normalized_percentile":{"value":0.99511719,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":87,"max":99},"biblio":{"volume":"1","issue":"1","first_page":"46","last_page":"52"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.6371999979019165,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.6371999979019165,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.18790000677108765,"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/T12029","display_name":"DNA and Biological Computing","score":0.1128000020980835,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sequencing-by-hybridization","display_name":"sequencing by hybridization","score":0.8840000033378601},{"id":"https://openalex.org/keywords/spectrum-acquisition","display_name":"spectrum acquisition","score":0.46799999475479126},{"id":"https://openalex.org/keywords/wildcards","display_name":"wildcards","score":0.6430000066757202},{"id":"https://openalex.org/keywords/probe-length","display_name":"probe length","score":0.6769999861717224},{"id":"https://openalex.org/keywords/universal-base","display_name":"universal base","score":0.7760000228881836},{"id":"https://openalex.org/keywords/dna-sequence-reconstruction","display_name":"DNA sequence reconstruction","score":0.6460000276565552}],"concepts":[{"id":"https://openalex.org/C156778621","wikidata":"https://www.wikidata.org/wiki/Q1365748","display_name":"Spectrum (functional analysis)","level":2,"score":0.544405460357666},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5322116613388062},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5143245458602905},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5128798484802246},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.42447537183761597},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4157964885234833},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35794949531555176},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.284185528755188},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25574660301208496},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17009970545768738},{"id":"https://openalex.org/C33332235","wikidata":"https://www.wikidata.org/wiki/Q18362","display_name":"Theoretical physics","level":1,"score":0.10990282893180847},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009693","descriptor_name":"Nucleic Acid Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D044366","descriptor_name":"Transition Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2004.12","doi":"https://doi.org/10.1109/tcbb.2004.12","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2004.12","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","dongbi-b","doyens","jufo-2","medline","norway-1","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17048407","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17048407","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,"listed_in":[],"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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.61.3111","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.61.3111","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.brown.edu/research/pubs/pdfs/2004/Preparata-2004-SHR.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309070","display_name":"Brown University","ror":"https://ror.org/05gq02987"},{"id":"https://openalex.org/F4320320698","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49"},{"id":"https://openalex.org/F4320332222","display_name":"University of Illinois at Urbana-Champaign","ror":"https://ror.org/047426m28"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1490430289","https://openalex.org/W1493192698","https://openalex.org/W1600463518","https://openalex.org/W1986088012","https://openalex.org/W1998971063","https://openalex.org/W2057452839","https://openalex.org/W2067422430","https://openalex.org/W2077095651","https://openalex.org/W2077433900","https://openalex.org/W2112780289","https://openalex.org/W2116791963","https://openalex.org/W2125181285","https://openalex.org/W2125882871","https://openalex.org/W2135343804","https://openalex.org/W2135995702","https://openalex.org/W2149681483","https://openalex.org/W2485066751","https://openalex.org/W2611121916","https://openalex.org/W2751862591","https://openalex.org/W2752786510","https://openalex.org/W4235512468","https://openalex.org/W6819064998"],"related_works":["https://openalex.org/W2046291777","https://openalex.org/W2057452839","https://openalex.org/W2035644421","https://openalex.org/W1987345132","https://openalex.org/W2058317409","https://openalex.org/W1967717237","https://openalex.org/W2246114146","https://openalex.org/W2611121916","https://openalex.org/W7101017023"],"abstract_inverted_index":{"All":[0],"published":[1],"approaches":[2,134],"to":[3,27,67,104,206],"DNA":[4],"sequencing":[5,78],"by":[6,33,83],"hybridization":[7,147],"(SBH)":[8],"consist":[9],"of":[10,14,17,23,37,55,61,100,129,146,191,209],"the":[11,15,34,38,44,49,59,89,98,105,112,126,154,165,172,182,207,224],"biochemical":[12,173,202],"acquisition":[13],"spectrum":[16,113],"a":[18,28,53,73,138,220],"target":[19],"sequence":[20,39],"(the":[21],"set":[22],"its":[24,41],"subsequences":[25],"conforming":[26],"given":[29],"probing":[30,50,90],"pattern)":[31],"followed":[32],"algorithmic":[35,108],"reconstruction":[36],"from":[40,153],"spectrum.":[42],"In":[43],"\"standard\"":[45],"or":[46],"\"uniform\"":[47],"approach,":[48],"pattern":[51],"is":[52,65,148,199],"string":[54],"length":[56,60,180],"L":[57],"and":[58,107],"reliably":[62],"reconstructible":[63],"sequences":[64],"known":[66],"be":[68,81,219],"mlen":[69],"=":[70,123],"O(2(L)).":[71],"For":[72],"fixed":[74],"microarray":[75],"area,":[76],"higher":[77],"performance":[79],"can":[80,120],"achieved":[82],"inserting":[84],"nonprobing":[85],"gaps":[86,106],"(\"wild-cards\")":[87],"in":[88,157,215],"pattern.":[91],"The":[92,144,211],"reconstruction,":[93],"however,":[94],"must":[95],"cope":[96],"with":[97],"emergence":[99],"fooling":[101],"probes":[102],"due":[103],"failure":[109],"occurs":[110],"when":[111],"becomes":[114],"too":[115],"densely":[116],"populated,":[117],"although":[118],"we":[119,160],"achieve":[121],"mcomp":[122],"0(4(L)).":[124],"Despite":[125],"combinatorial":[127],"success":[128,208],"gapped":[130],"probing,":[131],"all":[132],"current":[133],"are":[135,204],"based":[136],"on":[137],"biochemically":[139],"unrealistic":[140],"spectrum-acquisition":[141],"model":[142],"(digital-spectrum).":[143],"reality":[145],"much":[149],"more":[150,169],"complex.":[151],"Departing":[152],"conventional":[155],"model,":[156,167],"this":[158,216],"paper,":[159],"propose":[161],"an":[162],"alternative,":[163],"called":[164],"analog-spectrum":[166],"which":[168],"closely":[170],"reflects":[171],"process.":[174],"This":[175],"novel":[176],"modeling":[177],"reestablishes":[178],"probe":[179],"as":[181,188],"performance-governing":[183],"factor,":[184],"adopting":[185],"\"semidegenerate":[186],"bases\"":[187],"suitable":[189],"emulators":[190],"currently":[192],"inadequate":[193],"universal":[194],"bases.":[195],"One":[196],"important":[197],"conclusion":[198],"that":[200],"accurate":[201],"measurements":[203],"pivotal":[205],"SBH.":[210],"theoretical":[212],"proposal":[213],"presented":[214],"paper":[217],"should":[218],"convincing":[221],"stimulus":[222],"for":[223],"needed":[225],"biotechnological":[226],"work.":[227]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":12}],"updated_date":"2026-11-14T11:04:58.165337","created_date":"2016-06-24T00:00:00"}