Featured Publications
Control of cell state transitions
Rukhlenko O, Halasz M, Rauch N, Zhernovkov V, Prince T, Wynne K, Maher S, Kashdan E, MacLeod K, Carragher N, Kolch W, Kholodenko B. Control of cell state transitions. Nature 2022, 609: 975-985. PMID: 36104561, PMCID: PMC9644236, DOI: 10.1038/s41586-022-05194-y.Peer-Reviewed Original ResearchConceptsCell state transitionsCell fateCell statesCell fate transitionsCell fate decisionsSingle-cell dataNew biological insightsFate transitionsMovement of cellsFate decisionsWaddington landscapePhenotypic dataBiological insightsOmics datasetsOmics dataCellular modelMechanistic modelLandscape1FateCellsDevelopment pathwaysLandscapeBiologyState transitionsTherapeutic interventions
2021
Can Systems Biology Advance Clinical Precision Oncology?
Rocca A, Kholodenko B. Can Systems Biology Advance Clinical Precision Oncology? Cancers 2021, 13: 6312. PMID: 34944932, PMCID: PMC8699328, DOI: 10.3390/cancers13246312.Peer-Reviewed Original ResearchSignal transduction networksSystems biology studiesGenotype-phenotype relationshipsTransduction networksSystems biology modelsSystems biologyBiological processesEnvironmental perturbationsBiology studiesCancer mutationsNetwork reconstructionPrecision oncologyBiology modelsTumor molecular alterationsBiological systemsArray of techniquesMolecular alterationsIndividual cancer patientsOncological researchBiologyValuable toolMutationsTherapeutic treatment
2005
Mechanistic and modular approaches to modeling and inference of cellular regulatory networks
Kholodenko B, Bruggeman F, Sauro H. Mechanistic and modular approaches to modeling and inference of cellular regulatory networks. Topics In Current Genetics 2005, 13: 143-159. DOI: 10.1007/b136809.Peer-Reviewed Original ResearchReaction-diffusion equationsCellular regulatory networksRegulatory networksSystems biologyMolecular mechanismsBiochemical networksNetwork inferencePhysiological responsesNew insightsModeling approachChemical kineticsInferenceMolecular dynamics simulationsEquationsModelingBiologyComputational modelingNetworkModular approachDynamics simulationsApproachSimulationsNovel approach
2000
Metabolic Control From The Back Benches: Biochemistry Towards Biocomplexity
Westerhoff H, Teusink B, Mensonides F, Reijenga K, Esgalhado E, Kholodenko B, Somsen O, Van Heeswijk W, Boogerd F, Bruggeman F, Snoep J. Metabolic Control From The Back Benches: Biochemistry Towards Biocomplexity. NATO Science Partnership Subseries: 3 2000, 235-242. DOI: 10.1007/978-94-011-4072-0_26.Peer-Reviewed Original ResearchBacterial inner membraneElectron transfer chainImportant metabolic processesBiological free energy transductionFermentation of glucoseInner membraneATP hydrolysisPhysiological processesMetabolic processesMolecular biologyProton pumpLiving cellsStudy of metabolismProtein fractionsBiochemical reactionsIndependent chemical reactionsFree energy transductionBiochemistryChemical reactionsTransductionYeastBiocomplexityReactionBiologySubstantial progress
1995
HIERARCHIES IN CONTROL
JENSEN P, VAN DER GUGTEN A, BIER M, VAN HEESWIJK W, ROHWER J, MOLENAAR D, VAN WORKUM M, RICHARD P, TEUSINK B, BAKKER B, KHOLODENKO B, WESTERHOFF H. HIERARCHIES IN CONTROL. Journal Of Biological System 1995, 3: 139-144. DOI: 10.1142/s0218339095000137.Peer-Reviewed Original Research