{"id":"https://openalex.org/W2101712920","doi":"https://doi.org/10.1093/bioinformatics/bti144","title":"Solving and analyzing side-chain positioning problems using linear and integer programming","display_name":"Solving and analyzing side-chain positioning problems using linear and integer programming","publication_year":2004,"publication_date":"2004-11-16","ids":{"openalex":"https://openalex.org/W2101712920","doi":"https://doi.org/10.1093/bioinformatics/bti144","mag":"2101712920","pmid":"https://pubmed.ncbi.nlm.nih.gov/15546935"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/1028/48966796/bioinformatics_21_7_1028.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/1028/48966796/bioinformatics_21_7_1028.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029994273","display_name":"Carleton L. Kingsford","orcid":null},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Carleton L. Kingsford","raw_affiliation_strings":["Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ 08544, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ 08544, USA","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044565966","display_name":"Bernard Chazelle","orcid":"https://orcid.org/0000-0001-8542-0247"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernard Chazelle","raw_affiliation_strings":["Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ 08544, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ 08544, USA","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085615320","display_name":"Mona Singh","orcid":"https://orcid.org/0000-0001-8271-6026"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mona Singh","raw_affiliation_strings":["Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ 08544, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ 08544, USA","institution_ids":["https://openalex.org/I20089843"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5029994273"],"corresponding_institution_ids":["https://openalex.org/I20089843"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":8.8913,"has_fulltext":false,"cited_by_count":239,"citation_normalized_percentile":{"value":0.98238705,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"21","issue":"7","first_page":"1028","last_page":"1039"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10142","display_name":"Formal Methods in Verification","score":0.9660000205039978,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10142","display_name":"Formal Methods in Verification","score":0.9660000205039978,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12176","display_name":"Optimization and Packing Problems","score":0.9527000188827515,"subfield":{"id":"https://openalex.org/subfields/2209","display_name":"Industrial and Manufacturing Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12288","display_name":"Optimization and Search Problems","score":0.9520999789237976,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.7786904573440552},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6117931604385376},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.5967271327972412},{"id":"https://openalex.org/keywords/linear-programming","display_name":"Linear programming","score":0.5817837119102478},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.5220515727996826},{"id":"https://openalex.org/keywords/chain","display_name":"Chain (unit)","score":0.5000710487365723},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.378619521856308},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23105290532112122},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1984591782093048}],"concepts":[{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.7786904573440552},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6117931604385376},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.5967271327972412},{"id":"https://openalex.org/C41045048","wikidata":"https://www.wikidata.org/wiki/Q202843","display_name":"Linear programming","level":2,"score":0.5817837119102478},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.5220515727996826},{"id":"https://openalex.org/C199185054","wikidata":"https://www.wikidata.org/wiki/Q552299","display_name":"Chain (unit)","level":2,"score":0.5000710487365723},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.378619521856308},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23105290532112122},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1984591782093048},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009716","descriptor_name":"Numerical Analysis, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bti144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/1028/48966796/bioinformatics_21_7_1028.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15546935","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15546935","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.112.9945","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.112.9945","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.princeton.edu/~mona/Bioinformatics_SCP.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.646.6911","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.646.6911","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.princeton.edu/~chazelle/pubs/bioinfo04.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti144","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/1028/48966796/bioinformatics_21_7_1028.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8799999952316284,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1508596864","https://openalex.org/W1516916562","https://openalex.org/W1564062335","https://openalex.org/W1574312817","https://openalex.org/W1598984658","https://openalex.org/W1965205049","https://openalex.org/W1969845313","https://openalex.org/W1972728295","https://openalex.org/W1979404891","https://openalex.org/W1979938039","https://openalex.org/W1980745499","https://openalex.org/W1987977716","https://openalex.org/W1989916772","https://openalex.org/W2013238066","https://openalex.org/W2015403140","https://openalex.org/W2016038837","https://openalex.org/W2017994171","https://openalex.org/W2027189612","https://openalex.org/W2028843689","https://openalex.org/W2043883458","https://openalex.org/W2056257194","https://openalex.org/W2072969046","https://openalex.org/W2081044089","https://openalex.org/W2082221689","https://openalex.org/W2085497102","https://openalex.org/W2097649955","https://openalex.org/W2105321472","https://openalex.org/W2106315897","https://openalex.org/W2106775540","https://openalex.org/W2106882534","https://openalex.org/W2115942081","https://openalex.org/W2116214348","https://openalex.org/W2118116238","https://openalex.org/W2119894792","https://openalex.org/W2145896324","https://openalex.org/W2156469184","https://openalex.org/W2162215949","https://openalex.org/W2164750034","https://openalex.org/W2172114588","https://openalex.org/W2611076569","https://openalex.org/W2786741601","https://openalex.org/W2911275871","https://openalex.org/W6600379119"],"related_works":["https://openalex.org/W1925942709","https://openalex.org/W2047683846","https://openalex.org/W2044902158","https://openalex.org/W2082154838","https://openalex.org/W2109912052","https://openalex.org/W1711527768","https://openalex.org/W4295916115","https://openalex.org/W4285278887","https://openalex.org/W2995925505","https://openalex.org/W2365237642"],"abstract_inverted_index":{"MOTIVATION:":[0],"Side-chain":[1],"positioning":[2,72,116,213],"is":[3,22,36,39,184,192],"a":[4,14,28,32,44,88,127],"central":[5],"component":[6],"of":[7,17,70,178],"homology":[8],"modeling":[9],"and":[10,31,103,106,121],"protein":[11,112],"design.":[12,113],"In":[13],"common":[15],"formulation":[16,69],"the":[18,20,83,140,143,164,176,179,181,193,211],"problem,":[19,180],"backbone":[21],"fixed,":[23],"side-chain":[24,71,212],"conformations":[25],"come":[26],"from":[27],"rotamer":[29],"library,":[30],"pairwise":[33],"energy":[34,131,172],"function":[35,132],"optimized.":[37],"It":[38],"NP-complete":[40],"to":[41,48,53,76,86,97,107,186],"find":[42,187],"even":[43],"reasonable":[45],"approximate":[46],"solution":[47],"this":[49,55],"problem.":[50,214],"We":[51,62,81,94],"seek":[52],"put":[54],"hardness":[56],"result":[57],"into":[58],"practical":[59],"context.":[60],"RESULTS:":[61],"present":[63],"an":[64],"integer":[65],"linear":[66,90],"programming":[67,91],"(ILP)":[68],"that":[73,197],"allows":[74],"us":[75],"tackle":[77],"large":[78,157],"problem":[79,145],"sizes.":[80],"relax":[82],"integrality":[84],"constraint":[85],"give":[87],"polynomial-time":[89],"(LP)":[92],"heuristic.":[93],"apply":[95],"LP":[96,151],"position":[98],"side":[99,109,117],"chains":[100,110,118],"on":[101,119],"native":[102,120],"homologous":[104,122],"backbones":[105],"choose":[108],"for":[111,156,210],"Surprisingly,":[114],"when":[115],"backbones,":[123],"optimal":[124,154,188,205],"solutions":[125,155,209],"using":[126,137,150,163],"simple,":[128],"biologically":[129],"relevant":[130],"can":[133,159],"usually":[134],"be":[135,148,161],"found":[136,162],"LP.":[138],"On":[139],"other":[141],"hand,":[142],"design":[144],"often":[146],"cannot":[147],"solved":[149],"directly;":[152],"however,":[153],"instances":[158],"still":[160],"computationally":[165],"more":[166],"expensive":[167],"ILP":[168],"procedure.":[169],"While":[170],"different":[171],"functions":[173],"also":[174],"affect":[175],"difficulty":[177],"LP/ILP":[182],"approach":[183],"able":[185],"solutions.":[189],"Our":[190],"analysis":[191],"first":[194],"large-scale":[195],"demonstration":[196],"LP-based":[198],"approaches":[199],"are":[200],"highly":[201],"effective":[202],"in":[203],"finding":[204],"(and":[206],"successive":[207],"near-optimal)":[208]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":42},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":15}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
