{"id":"https://openalex.org/W2040143682","doi":"https://doi.org/10.1186/1752-0509-6-119","title":"An integer optimization algorithm for robust identification of non-linear gene regulatory networks","display_name":"An integer optimization algorithm for robust identification of non-linear gene regulatory networks","publication_year":2012,"publication_date":"2012-09-02","ids":{"openalex":"https://openalex.org/W2040143682","doi":"https://doi.org/10.1186/1752-0509-6-119","mag":"2040143682","pmid":"https://pubmed.ncbi.nlm.nih.gov/22937832","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3444924"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-119","doi":"https://doi.org/10.1186/1752-0509-6-119","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-119","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-119","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-119","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026413302","display_name":"Nishanth Gopalakrishnan Chemmangattuvalappil","orcid":"https://orcid.org/0000-0002-1501-7441","observed_orcids":["https://orcid.org/0000-0002-1501-7441"]},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nishanth Chemmangattuvalappil","raw_affiliation_strings":["Department of Chemical Engineering, University of Pittsburgh, 1249 Benedum Hall, 3700 O'Hara Street, Pittsburgh, PA 15261, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Pittsburgh, 1249 Benedum Hall, 3700 O'Hara Street, Pittsburgh, PA 15261, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032755922","display_name":"Keith Task","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keith Task","raw_affiliation_strings":["Department of Chemical Engineering, University of Pittsburgh, 1249 Benedum Hall, 3700 O\u2019Hara Street, Pittsburgh, PA, 15261, USA","Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Pittsburgh, 1249 Benedum Hall, 3700 O\u2019Hara Street, Pittsburgh, PA, 15261, USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087175427","display_name":"Ipsita Banerjee","orcid":"https://orcid.org/0000-0001-6791-3646","observed_orcids":["https://orcid.org/0000-0001-6791-3646"]},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ipsita Banerjee","raw_affiliation_strings":["Department of Chemical Engineering, University of Pittsburgh, 1249 Benedum Hall, 3700 O\u2019Hara Street, Pittsburgh, PA, 15261, USA","Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Pittsburgh, 1249 Benedum Hall, 3700 O\u2019Hara Street, Pittsburgh, PA, 15261, USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087175427"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":0.7706,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.68357026,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"6","issue":"1","first_page":"119","last_page":"119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":1.0,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":1.0,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.0,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0,"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/gene-regulatory-network-inference","display_name":"gene regulatory network inference","score":0.9769999980926514},{"id":"https://openalex.org/keywords/integer-programming","display_name":"integer programming","score":0.7160000205039978},{"id":"https://openalex.org/keywords/s-system","display_name":"S-systems","score":0.5619999766349792},{"id":"https://openalex.org/keywords/bootstrap-method","display_name":"bootstrapping","score":0.8849999904632568},{"id":"https://openalex.org/keywords/temporal-gene-expression","display_name":"temporal gene expression","score":0.7770000100135803},{"id":"https://openalex.org/keywords/experimental-noise","display_name":"experimental noise","score":0.7229999899864197},{"id":"https://openalex.org/keywords/network-sparsity","display_name":"network sparsity","score":0.8659999966621399},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.8500000238418579}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6809993982315063},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6132458448410034},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5932772159576416},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.582094132900238},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5393801331520081},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5155770182609558},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.47772690653800964},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.43337109684944153},{"id":"https://openalex.org/C119247159","wikidata":"https://www.wikidata.org/wiki/Q1366192","display_name":"System identification","level":3,"score":0.4196382164955139},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.415536105632782},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3195987939834595},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20251789689064026},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.1796703338623047},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16964057087898254},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004260","descriptor_name":"DNA Repair","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","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":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-6-119","doi":"https://doi.org/10.1186/1752-0509-6-119","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-119","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-119","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2448854","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3444924","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3444924","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3444924","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Syst Biol","raw_type":"Text"},{"id":"pmid:22937832","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22937832","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":"BMC systems biology","raw_type":"Journal Article"},{"id":"pmh:oai:d-scholarship.pitt.edu:29842","doi":null,"is_oa":false,"landing_page_url":"https://d-scholarship.pitt.edu/29842/7/licence.txt","pdf_url":null,"source":{"id":"https://openalex.org/S4306402372","display_name":"D-Scholarship@Pitt (University of Pittsburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I170201317","host_organization_name":"University of Pittsburgh","host_organization_lineage":["https://openalex.org/I170201317"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-119","doi":"https://doi.org/10.1186/1752-0509-6-119","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-119","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-119","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G6020705441","display_name":null,"funder_award_id":"DP2-16520","funder_id":"https://openalex.org/F4320337383","funder_display_name":"National Center for Chronic Disease Prevention and Health Promotion"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337383","display_name":"National Center for Chronic Disease Prevention and Health Promotion","ror":"https://ror.org/021rths28"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2040143682.pdf","grobid_xml":"https://content.openalex.org/works/W2040143682.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W609513197","https://openalex.org/W1598590531","https://openalex.org/W1996264210","https://openalex.org/W2018435536","https://openalex.org/W2053913299","https://openalex.org/W2058670155","https://openalex.org/W2069323107","https://openalex.org/W2090554117","https://openalex.org/W2096359570","https://openalex.org/W2100169396","https://openalex.org/W2104676838","https://openalex.org/W2113979998","https://openalex.org/W2114937915","https://openalex.org/W2115108153","https://openalex.org/W2118891267","https://openalex.org/W2122342005","https://openalex.org/W2123584272","https://openalex.org/W2126874285","https://openalex.org/W2134978629","https://openalex.org/W2136988691","https://openalex.org/W2141239733","https://openalex.org/W2142170851","https://openalex.org/W2149635958","https://openalex.org/W2158214348","https://openalex.org/W2159495578","https://openalex.org/W2159717709","https://openalex.org/W2160482844","https://openalex.org/W2160533336","https://openalex.org/W2161304688","https://openalex.org/W2161409973","https://openalex.org/W2161511352","https://openalex.org/W2166106382","https://openalex.org/W3106889297"],"related_works":["https://openalex.org/W1993189701","https://openalex.org/W1496513776","https://openalex.org/W7097358967","https://openalex.org/W1963842580","https://openalex.org/W2103673431","https://openalex.org/W2002085380","https://openalex.org/W4213337311","https://openalex.org/W2189319041","https://openalex.org/W1520746228","https://openalex.org/W2009292718"],"abstract_inverted_index":{"BACKGROUND:":[0],"Reverse":[1],"engineering":[2],"gene":[3,30,96,147,207,269,295,302,328],"networks":[4,297],"and":[5,69,88,106,205,218,232,245,247,253,263,308,331,341],"identifying":[6],"regulatory":[7,31,91,296,329],"interactions":[8,92,133],"are":[9,57,61,272],"integral":[10],"to":[11,63,82,139,190,196,292,312,327,349],"understanding":[12],"cellular":[13],"decision":[14],"making":[15],"processes.":[16],"Advancement":[17],"in":[18,66,71,99,118,146,216,237,258,261,273,339],"high":[19,243],"throughput":[20],"experimental":[21,42,104,136,204,219,264],"techniques":[22],"has":[23,335],"initiated":[24],"innovative":[25],"data":[26,98,116],"driven":[27],"analysis":[28],"of":[29,49,90,102,161,163,199,235,280,321],"networks.":[32],"However,":[33],"inherent":[34,311],"noise":[35,105,307],"associated":[36],"with":[37,125,277,318],"biological":[38,55,119,164,313,351],"systems":[39,120],"requires":[40],"numerous":[41],"replicates":[43,137],"for":[44,181],"reliable":[45],"conclusions.":[46],"Furthermore,":[47,141,257],"evidence":[48],"robust":[50,70,132,294],"algorithms":[51,60],"directly":[52],"exploiting":[53],"basic":[54,154],"traits":[56],"few.":[58],"Such":[59],"expected":[62],"be":[64,347],"efficient":[65],"their":[67,72],"performance":[68],"prediction.":[73],"RESULTS:":[74],"We":[75],"have":[76,114,143],"developed":[77,210],"a":[78],"network":[79,123,155,183,193,322],"identification":[80,124,156,169],"algorithm":[81,170,211,226,288],"accurately":[83,228],"infer":[84],"both":[85,215,259],"the":[86,100,126,150,159,168,192,197,203,225,230,236,251,260,267,278,281,315,319,333],"topology":[87,231],"strength":[89,234],"from":[93,134,298],"time":[94],"series":[95],"expression":[97,270,303],"presence":[101],"significant":[103,306],"non-linear":[107,300],"behavior.":[108],"In":[109],"this":[110],"novel":[111],"formulism,":[112,317],"we":[113,142],"addressed":[115],"variability":[117],"by":[121,177,242],"integrating":[122],"bootstrap":[127],"resampling":[128],"technique,":[129],"hence":[130],"predicting":[131],"limited":[135],"subjected":[138,195],"noise.":[140],"incorporated":[144],"non-linearity":[145],"dynamics":[148,279],"using":[149,214],"S-system":[151],"formulation.":[152],"The":[153,185,209],"formulation":[157,334],"exploits":[158],"trait":[160],"sparsity":[162],"interactions.":[165],"Towards":[166],"that,":[167],"is":[171,188,212,324],"formulated":[172],"as":[173,240],"an":[174],"integer-programming":[175],"problem":[176],"introducing":[178],"binary":[179],"variables":[180],"each":[182],"component.":[184],"objective":[186],"function":[187],"targeted":[189],"minimize":[191],"connections":[194],"constraint":[198],"maximal":[200],"agreement":[201,276],"between":[202,250],"predicted":[206,254,268],"dynamics.":[208],"validated":[213,337],"silico":[217,238,262,340],"data-sets.":[220],"These":[221],"studies":[222],"show":[223],"that":[224],"can":[227,346],"predict":[229],"connection":[233],"networks,":[239,330],"quantified":[241],"precision":[244],"recall,":[246],"small":[248],"discrepancy":[249],"actual":[252],"kinetic":[255],"parameters.":[256],"case":[265],"studies,":[266],"profiles":[271],"very":[274],"close":[275],"input":[282],"data.":[283,304],"CONCLUSIONS:":[284],"Our":[285],"integer":[286],"programming":[287],"effectively":[289],"utilizes":[290],"bootstrapping":[291],"identify":[293],"noisy,":[299],"time-series":[301],"With":[305],"non-linearities":[309],"being":[310],"systems,":[314],"present":[316],"incorporation":[320],"sparsity,":[323],"extremely":[325],"relevant":[326],"while":[332],"been":[336],"against":[338],"E.":[342],"Coli":[343],"data,":[344],"it":[345],"applied":[348],"any":[350],"system.":[352]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}