{"id":"https://openalex.org/W6977516638","doi":"https://doi.org/10.6084/m9.figshare.c.3789970","title":"Supplementary material from \"A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths\"","display_name":"Supplementary material from \"A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths\"","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W6977516638","doi":"https://doi.org/10.6084/m9.figshare.c.3789970","mag":"2618411380"},"language":"en","primary_location":{"id":"doi:10.6084/m9.figshare.c.3789970","doi":"https://doi.org/10.6084/m9.figshare.c.3789970","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.3789970","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Collection"},"volume":null,"type":"supplementary-materials","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.6084/m9.figshare.c.3789970","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Olariu, Victor","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Olariu, Victor","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071106967","display_name":"Erica Manesso","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Manesso, Erica","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5057866050","display_name":"Carsten Peterson","orcid":"https://orcid.org/0000-0001-7362-2191","observed_orcids":["https://orcid.org/0000-0001-7362-2191"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Peterson, Carsten","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9990000128746033,"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":0.9990000128746033,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":9.999999747378752e-05,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/free-energy-landscape","display_name":"free energy landscape","score":0.8479999899864197},{"id":"https://openalex.org/keywords/gene-networks","display_name":"gene networks","score":0.6819999814033508},{"id":"https://openalex.org/keywords/lineage-commitment","display_name":"lineage commitment","score":0.8309999704360962},{"id":"https://openalex.org/keywords/cellular-reprogramming","display_name":"cellular reprogramming","score":0.9789999723434448},{"id":"https://openalex.org/keywords/shortest-path-algorithms","display_name":"shortest path algorithms","score":0.75},{"id":"https://openalex.org/keywords/michaelis-menten-kinetics","display_name":"Michaelis-Menten kinetics","score":0.8550000190734863},{"id":"https://openalex.org/keywords/hematopoiesis","display_name":"hematopoiesis","score":0.8299999833106995},{"id":"https://openalex.org/keywords/gene-regulatory-circuits","display_name":"gene regulatory circuits","score":0.5839999914169312}],"concepts":[{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.5993000268936157},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.5806000232696533},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5447999835014343},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.49559998512268066},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4659000039100647},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.42289999127388},{"id":"https://openalex.org/C77255625","wikidata":"https://www.wikidata.org/wiki/Q402093","display_name":"Reprogramming","level":3,"score":0.37049999833106995},{"id":"https://openalex.org/C2780165032","wikidata":"https://www.wikidata.org/wiki/Q16869822","display_name":"Energy consumption","level":2,"score":0.335999995470047},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3222000002861023},{"id":"https://openalex.org/C2986044853","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Genetic network","level":3,"score":0.3142000138759613},{"id":"https://openalex.org/C22590252","wikidata":"https://www.wikidata.org/wiki/Q1058754","display_name":"Shortest path problem","level":3,"score":0.3138999938964844},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.3082999885082245},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.2971000075340271},{"id":"https://openalex.org/C81388566","wikidata":"https://www.wikidata.org/wiki/Q526668","display_name":"Sigmoid function","level":3,"score":0.29600000381469727},{"id":"https://openalex.org/C128849468","wikidata":"https://www.wikidata.org/wiki/Q1341258","display_name":"Energy budget","level":2,"score":0.2721000015735626},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.27129998803138733},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.2696000039577484},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2678999900817871},{"id":"https://openalex.org/C8272713","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Stochastic process","level":2,"score":0.26759999990463257},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2581000030040741},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.2574999928474426}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.6084/m9.figshare.c.3789970","doi":"https://doi.org/10.6084/m9.figshare.c.3789970","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.3789970","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Collection"},{"id":"doi:10.6084/m9.figshare.c.3789970.v1","doi":"https://doi.org/10.6084/m9.figshare.c.3789970.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.3789970.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Collection"},{"id":"mag:2618411380","doi":null,"is_oa":false,"landing_page_url":"https://figshare.com/collections/Supplementary_material_from_A_deterministic_method_for_estimating_free_energy_genetic_network_landscapes_with_applications_to_cell_commitment_and_reprogramming_paths_/3789970","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.6084/m9.figshare.c.3789970","doi":"https://doi.org/10.6084/m9.figshare.c.3789970","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.3789970","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Collection"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2624221999","https://openalex.org/W6977184542","https://openalex.org/W4285498302","https://openalex.org/W7100712290","https://openalex.org/W2056827131","https://openalex.org/W2035824523","https://openalex.org/W2672643241","https://openalex.org/W3150060768","https://openalex.org/W3035881769","https://openalex.org/W2545929049"],"abstract_inverted_index":{"Depicting":[0],"developmental":[1],"processes":[2],"as":[3],"movements":[4],"in":[5,149],"free":[6,31,99,116,132],"energy":[7,32,49,100,117,133],"genetic":[8],"landscapes":[9,17,50],"is":[10,25],"an":[11],"illustrative":[12],"tool.":[13],"However,":[14],"exploring":[15],"such":[16,131],"to":[18,35,145,179],"obtain":[19],"quantitative":[20],"or":[21,39,128],"even":[22],"qualitative":[23],"predictions":[24],"hampered":[26],"by":[27,52],"the":[28,36,44,61,115,150,154,174],"lack":[29],"of":[30,63,74,105,119,121,185],"functions":[33],"corresponding":[34],"biochemical":[37],"Michaelis\u2013Menten":[38],"Hill":[40],"rate":[41,83,94,106],"equations":[42,84,95],"for":[43,85,113,159,166,183,189],"dynamics.":[45],"Being":[46],"armed":[47],"with":[48,82],"defined":[51],"a":[53,110,141],"network":[54],"and":[55,68,161,168,171],"its":[56],"interactions":[57],"would":[58],"open":[59],"up":[60],"possibility":[62],"swiftly":[64],"identifying":[65],"cell":[66,75,164],"states":[67],"computing":[69],"optimal":[70,147],"paths,":[71],"including":[72],"those":[73],"reprogramming,":[76],"thereby":[77],"avoiding":[78],"exhaustive":[79],"trial-and-error":[80],"simulations":[81],"different":[86,125],"parameter":[87],"sets.":[88],"It":[89],"turns":[90],"out":[91],"that":[92],"sigmoidal":[93],"do":[96],"have":[97,136],"approximate":[98],"associations.":[101],"With":[102],"this":[103],"replacement":[104],"equations,":[107],"we":[108,139],"develop":[109],"deterministic":[111],"method":[112,155,175],"estimating":[114],"surfaces":[118],"systems":[120],"interacting":[122],"genes":[123],"at":[124],"noise":[126],"levels":[127],"temperatures.":[129],"Once":[130],"landscape":[134],"estimates":[135],"been":[137],"established,":[138],"adapt":[140],"shortest":[142],"path":[143],"algorithm":[144],"determine":[146,180],"routes":[148],"landscapes.":[151],"We":[152],"explore":[153],"on":[156],"three":[157],"circuits":[158],"haematopoiesis":[160],"embryonic":[162],"stem":[163],"development":[165],"commitment":[167],"reprogramming":[169],"scenarios":[170],"illustrate":[172],"how":[173],"can":[176],"be":[177],"used":[178],"sequential":[181],"steps":[182],"onsets":[184],"external":[186],"factors,":[187],"essential":[188],"efficient":[190],"reprogramming.":[191]},"counts_by_year":[],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2025-10-10T00:00:00"}
