{"id":"https://openalex.org/W4280553729","doi":"https://doi.org/10.1093/bioinformatics/btac318","title":"Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation","display_name":"Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation","publication_year":2022,"publication_date":"2022-05-09","ids":{"openalex":"https://openalex.org/W4280553729","doi":"https://doi.org/10.1093/bioinformatics/btac318","pmid":"https://pubmed.ncbi.nlm.nih.gov/35554499"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac318","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/14/3676/49883843/btac318.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"letter","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/14/3676/49883843/btac318.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001364288","display_name":"Felix M. Weidner","orcid":"https://orcid.org/0000-0001-6759-0509"},"institutions":[{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"education","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Felix M Weidner","raw_affiliation_strings":["Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany","International Graduate School of Molecular Medicine, Ulm University , 89081 Ulm, Germany"],"raw_orcid":"https://orcid.org/0000-0001-6759-0509","affiliations":[{"raw_affiliation_string":"Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]},{"raw_affiliation_string":"International Graduate School of Molecular Medicine, Ulm University , 89081 Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000170757","display_name":"Julian Schwab","orcid":"https://orcid.org/0000-0002-3050-0618"},"institutions":[{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"education","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Julian D Schwab","raw_affiliation_strings":["Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026604102","display_name":"Silke D Werle","orcid":"https://orcid.org/0000-0002-5153-0269"},"institutions":[{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"education","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Silke D Werle","raw_affiliation_strings":["Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024172459","display_name":"Nensi Ikonomi","orcid":"https://orcid.org/0000-0003-0780-5832"},"institutions":[{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"education","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nensi Ikonomi","raw_affiliation_strings":["Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany","International Graduate School of Molecular Medicine, Ulm University , 89081 Ulm, Germany"],"raw_orcid":"https://orcid.org/0000-0003-0780-5832","affiliations":[{"raw_affiliation_string":"Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]},{"raw_affiliation_string":"International Graduate School of Molecular Medicine, Ulm University , 89081 Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025725951","display_name":"Ludwig Lausser","orcid":null},"institutions":[{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"education","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ludwig Lausser","raw_affiliation_strings":["Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023316486","display_name":"Hans A. Kestler","orcid":"https://orcid.org/0000-0002-4759-5254"},"institutions":[{"id":"https://openalex.org/I196349391","display_name":"Universit\u00e4t Ulm","ror":"https://ror.org/032000t02","country_code":"DE","type":"education","lineage":["https://openalex.org/I196349391"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Hans A Kestler","raw_affiliation_strings":["Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4759-5254","affiliations":[{"raw_affiliation_string":"Institute of Medical Systems Biology, Ulm University , 89081 Ulm, Germany","institution_ids":["https://openalex.org/I196349391"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5023316486"],"corresponding_institution_ids":["https://openalex.org/I196349391"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"38","issue":"14","first_page":"3676","last_page":"3676"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9871000051498413,"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/T10581","display_name":"Neural dynamics and brain function","score":0.9846000075340271,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6534798741340637},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4789198637008667},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.4113270044326782},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23017925024032593},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08536127209663391}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6534798741340637},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4789198637008667},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.4113270044326782},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23017925024032593},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08536127209663391},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac318","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/14/3676/49883843/btac318.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35554499","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35554499","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":"Comment"},{"id":"pmh:oai:pubmedcentral.nih.gov:9272794","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9272794","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac318","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/14/3676/49883843/btac318.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4280553729.pdf","grobid_xml":"https://content.openalex.org/works/W4280553729.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2103454055","https://openalex.org/W2799849816","https://openalex.org/W3161900583","https://openalex.org/W3199213843"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W2530322880"],"abstract_inverted_index":{"In":[0,39,129],"his":[1],"letter":[2],"to":[3,44,91,93,200,241,263],"the":[4,9,41,51,62,69,79,82,94,118,153,166,183,211,226,252,259,266,286],"editor,":[5],"Luis":[6],"Rocha":[7],"addresses":[8],"concern":[10],"that":[11,143],"other":[12],"researchers":[13],"might":[14],"be":[15,242,270],"discouraged":[16],"from":[17,30],"further":[18],"investigation":[19],"of":[20,53,71,81,85,107,117,155,168,213,223,234,245,261,285,306,317,328,345],"dynamic":[21,54,105,144,157,208,246],"analyses":[22,116,209,275],"in":[23,47,56,68,97,131,172,180,210,225,251],"Boolean":[24,58,72,173,206],"networks":[25,313],"based":[26,276],"on":[27,50,64,78,277,326],"a":[28,45,163,220,243,249],"statement":[29],"our":[31,48,86,98,132,194],"recently":[32],"published":[33],"manuscript":[34],"(Weidner":[35],"et":[36,290,320],"al.,":[37,291,321],"2021).":[38],"particular,":[40],"author":[42],"refers":[43],"phrase":[46],"abstract":[49],"feasibility":[52,167],"investigations":[55],"large":[57,311],"models.":[59,175],"We":[60],"value":[61],"discussion":[63],"this":[65,187],"crucial":[66],"topic":[67],"field":[70],"networks.":[73],"However,":[74],"we":[75,89,101,134,177],"kindly":[76],"disagree":[77],"interpretation":[80],"respective":[83],"parts":[84],"manuscript.":[87,195],"First,":[88],"want":[90],"refer":[92],"point":[95],"addressed":[96],"abstract.":[99],"Here,":[100,176],"state:":[102],"\u2018However,":[103],"since":[104],"complexity":[106,145],"these":[108],"models":[109],"grows":[110],"exponentially":[111,147],"with":[112,148,162,182,219,310],"their":[113],"size,":[114,150],"exhaustive":[115,169,214],"dynamics":[119],"and":[120,186,228,298,333],"consequently":[121],"screening":[122,201,215,253,296,325],"all":[123],"possible":[124],"interventions":[125,203,262],"eventually":[126],"becomes":[127,331],"infeasible\u2019.":[128],"addition,":[130],"introduction,":[133],"report":[135],"that:":[136],"\u2018Nevertheless,":[137],"also":[138,189],"for":[139,254],"BNs,":[140],"it":[141,198],"holds":[142],"scales":[146],"network":[149,174,278],"again":[151],"limiting":[152],"possibility":[154],"complete":[156],"investigations\u2019.":[158],"This":[159],"sentence":[160],"comes":[161,199],"reference":[164],"explaining":[165],"attractor":[170,287,329],"computation":[171],"are":[178],"entirely":[179],"line":[181],"view":[184],"given,":[185],"is":[188,191],"what":[190],"elaborated":[192],"throughout":[193],"Foremost,":[196],"when":[197,302],"potential":[202,229],"targets":[204,230,268],"using":[205],"networks,":[207],"sense":[212],"become":[216,338],"very":[217],"complex":[218],"growing":[221],"number":[222,260],"compounds":[224],"model":[227],"or":[231,293,314],"even":[232,315],"combinations":[233],"targets.":[235],"Our":[236],"method":[237],"does":[238],"not":[239],"aim":[240],"replacement":[244],"analysis":[247],"but":[248],"step":[250],"intervention":[255,324],"targets,":[256],"scaling":[257],"down":[258],"screen.":[264],"Subsequently,":[265],"identified":[267],"can":[269],"evaluated":[271],"by":[272],"different":[273],"perturbation":[274],"dynamics,":[279],"such":[280,308],"as":[281,309],"more":[282],"detailed":[283,323],"studies":[284],"landscape":[288],"(M\u00fcssel":[289],"2010),":[292],"an":[294],"automated":[295],"(Schwab":[297,319],"Kestler,":[299],"2018).":[300],"Especially":[301],"adding":[303],"another":[304],"layer":[305],"complexity,":[307],"reconstructed":[312],"populations":[316],"those":[318],"2021),":[322],"top":[327],"evaluation":[330],"complex,":[332],"interaction":[334],"graph-based":[335],"pre-screening":[336],"methods":[337],"helpful.":[339],"Financial":[340],"Support:":[341],"none":[342,347],"declared.":[343,348],"Conflict":[344],"Interest:":[346]},"counts_by_year":[],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2025-10-10T00:00:00"}
