{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T18:08:28Z","timestamp":1774980508014,"version":"3.50.1"},"reference-count":97,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T00:00:00Z","timestamp":1774915200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["I 5234-B"],"award-info":[{"award-number":["I 5234-B"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["DOC 111-B"],"award-info":[{"award-number":["DOC 111-B"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Research in multiome data integration comes with the challenge of high-dimensionality and a small sample size in time series data. Traditional statistical tools often fail to capture true functional modules in large molecular networks, resulting in spurious associations. Dynamical systems theory overcomes this hurdle by assuming the biological system follows a trajectory that can be modelled in such a way that the interactions in the network have a causal nature and pertain to mechanistic processes. Here we use kernel-DMD, a data-driven dynamical systems tool for time series data, for multiome network integration in the exotic plant species\n                    <jats:italic>Clusia<\/jats:italic>\n                    . We uncover differing modes of photosynthesis that correspond to the C3-like or strong CAM dynamics of two species,\n                    <jats:italic>Clusia major<\/jats:italic>\n                    and\n                    <jats:italic>Clusia rosea<\/jats:italic>\n                    and implement a control strategy that enables the\n                    <jats:italic>in silico<\/jats:italic>\n                    \u00a0phenocopying between the two species. We demonstrate the applicability of the Koopman operator to multiome data integration, uncover drivers of plasticity in molecular networks and also identify key biomarkers that could potentially establish more resilient forms of photosynthesis, such as CAM, for the introduction of new crop bioengineering possibilities in C3 plants.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1014029","type":"journal-article","created":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T17:31:27Z","timestamp":1774978287000},"page":"e1014029","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Kernel-DMD for multiome data integration and control"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-6139-6229","authenticated-orcid":true,"given":"Iro","family":"Pierides","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hannes 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Ann","year":"2025","journal-title":"EGUsphere"},{"issue":"1","key":"pcbi.1014029.ref021","doi-asserted-by":"crossref","first-page":"23489","DOI":"10.1038\/s41598-025-07255-4","article-title":"Dynamic mode decomposition for analysis and prediction of metabolic oscillations from time-lapse imaging of cellular autofluorescence","volume":"15","author":"D W\u00fcstner","year":"2025","journal-title":"Sci Rep"},{"issue":"5","key":"pcbi.1014029.ref022","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1080\/01691864.2014.981292","article-title":"Estimation of perturbations in robotic behavior using dynamic mode decomposition","volume":"29","author":"E Berger","year":"2015","journal-title":"Advanced Robotics"},{"issue":"3","key":"pcbi.1014029.ref023","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1007\/s00332-010-9087-5","article-title":"Coherent Swing Instability of Power Grids","volume":"21","author":"Y Susuki","year":"2011","journal-title":"J Nonlinear 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Sun","year":"2012","journal-title":"Metabolomics"},{"key":"pcbi.1014029.ref030","doi-asserted-by":"crossref","DOI":"10.1017\/9781009089517","volume-title":"Data-driven science and engineering: machine learning, dynamical systems, and control","author":"SL Brunton","year":"2022"},{"issue":"4","key":"pcbi.1014029.ref031","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0092299","article-title":"Solving the differential biochemical Jacobian from metabolomics covariance data","volume":"9","author":"T N\u00e4gele","year":"2014","journal-title":"PLoS One"},{"issue":"5","key":"pcbi.1014029.ref032","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1016\/j.celrep.2020.01.011","article-title":"Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation","volume":"30","author":"JL Wilson","year":"2020","journal-title":"Cell Reports"},{"issue":"7","key":"pcbi.1014029.ref033","article-title":"COVRECON: automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks","volume":"39","author":"J Li","year":"2023","journal-title":"Bioinformatics"},{"issue":"5","key":"pcbi.1014029.ref034","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1038\/s41423-024-01134-0","article-title":"Targeting PHGDH reverses the immunosuppressive phenotype of tumor-associated macrophages through \u03b1-ketoglutarate and mTORC1 signaling","volume":"21","author":"Z Cai","year":"2024","journal-title":"Cell Mol Immunol"},{"key":"pcbi.1014029.ref035","first-page":"188","article-title":"Challenges of inversely estimating Jacobian from metabolomics data","volume":"3","author":"X Sun","year":"2015","journal-title":"Frontiers in Bioengineering and Biotechnology"},{"key":"pcbi.1014029.ref036","doi-asserted-by":"crossref","first-page":"111055","DOI":"10.1016\/j.jtbi.2022.111055","article-title":"Inference on the structure of gene 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Williams","year":"2015","journal-title":"J Nonlinear Sci"},{"issue":"4","key":"pcbi.1014029.ref040","doi-asserted-by":"crossref","first-page":"433","DOI":"10.3934\/ammc.2024022","article-title":"StOKeDMD: Streaming Occupation kernel dynamic mode decomposition","volume":"2","author":"EH Gonzalez","year":"2024","journal-title":"AMMC"},{"key":"pcbi.1014029.ref041","author":"E Gonzalez","year":"2021","journal-title":"The kernel perspective on dynamic mode decomposition"},{"issue":"2","key":"pcbi.1014029.ref042","doi-asserted-by":"crossref","first-page":"247","DOI":"10.3934\/jcd.2015005","article-title":"A kernel-based method for data-driven koopman spectral analysis","volume":"2","author":"MO Williams","year":"2015","journal-title":"JCD"},{"key":"pcbi.1014029.ref043","volume-title":"A parametric framework for kernel-based dynamic mode decomposition using deep learning","author":"K Kevopoulos","year":"2024"},{"issue":"2271","key":"pcbi.1014029.ref044","doi-asserted-by":"crossref","DOI":"10.1098\/rspa.2022.0576","article-title":"Physics-informed dynamic mode decomposition","volume":"479","author":"PJ Baddoo","year":"2023","journal-title":"Proc R Soc A"},{"key":"pcbi.1014029.ref045","author":"N Panda","year":"2025","journal-title":"Kernel dynamic mode decomposition for sparse reconstruction of closable Koopman operators"},{"key":"pcbi.1014029.ref046","doi-asserted-by":"crossref","DOI":"10.1201\/9780429283321","volume-title":"An introduction to systems biology: design principles of biological circuits: Chapman and Hall\/CRC","author":"U Alon","year":"2019"},{"issue":"7","key":"pcbi.1014029.ref047","doi-asserted-by":"crossref","first-page":"1829","DOI":"10.1093\/jxb\/ern080","article-title":"On the nature of facultative and constitutive CAM: environmental and developmental control of CAM expression during early growth of Clusia, Kalanch\u00f6e, and Opuntia","volume":"59","author":"K Winter","year":"2008","journal-title":"J Exp Bot"},{"key":"pcbi.1014029.ref048","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.automatica.2018.03.046","article-title":"Linear predictors for nonlinear dynamical systems: Koopman operator meets model predictive control","volume":"93","author":"M Korda","year":"2018","journal-title":"Automatica"},{"key":"pcbi.1014029.ref049","author":"L Bold","year":"2025"},{"key":"pcbi.1014029.ref050","article-title":"Biosystems design to accelerate C3-to-CAM progression","author":"G Yuan","year":"2020","journal-title":"BioDesign Research"},{"issue":"2","key":"pcbi.1014029.ref051","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1137\/21M1401243","article-title":"Modern Koopman Theory for Dynamical Systems","volume":"64","author":"SL Brunton","year":"2022","journal-title":"SIAM Rev"},{"key":"pcbi.1014029.ref052","volume-title":"Notes on koopman operator theory","author":"SL Brunton","year":"2019"},{"key":"pcbi.1014029.ref053","doi-asserted-by":"crossref","first-page":"160","DOI":"10.3389\/fgene.2015.00160","article-title":"Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development","volume":"6","author":"J Davila-Velderrain","year":"2015","journal-title":"Front Genet"},{"key":"pcbi.1014029.ref054","article-title":"Sparsity-promoting algorithms for the discovery of informative Koopman-invariant subspaces","volume":"917","author":"S Pan","year":"2021","journal-title":"J Fluid Mech"},{"key":"pcbi.1014029.ref055","doi-asserted-by":"crossref","first-page":"3735","DOI":"10.1016\/j.csbj.2021.06.030","article-title":"Integration strategies of multi-omics data for machine learning analysis","volume":"19","author":"M Picard","year":"2021","journal-title":"Comput Struct Biotechnol J"},{"issue":"1","key":"pcbi.1014029.ref056","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/s13040-024-00406-9","article-title":"Supervised multiple kernel learning approaches for multi-omics data integration","volume":"17","author":"M Briscik","year":"2024","journal-title":"BioData Min"},{"key":"pcbi.1014029.ref057","volume-title":"A review of kernel methods in machine learning","author":"T Hofmann","year":"2006"},{"issue":"39","key":"pcbi.1014029.ref058","doi-asserted-by":"crossref","first-page":"8264","DOI":"10.1021\/bi201284u","article-title":"The original Michaelis constant: translation of the 1913 Michaelis-Menten paper","volume":"50","author":"L Michaelis","year":"2011","journal-title":"Biochemistry"},{"issue":"6","key":"pcbi.1014029.ref059","doi-asserted-by":"crossref","first-page":"160765","DOI":"10.1098\/rsos.160765","article-title":"A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths","volume":"4","author":"V Olariu","year":"2017","journal-title":"R Soc Open Sci"},{"issue":"9","key":"pcbi.1014029.ref060","doi-asserted-by":"crossref","first-page":"6189","DOI":"10.1109\/TSMC.2025.3578348","article-title":"FMvPCI: A Multiview Fusion Neural Network for Identifying Protein Complex via Fuzzy Clustering","volume":"55","author":"Y Yang","year":"2025","journal-title":"IEEE Trans Syst Man Cybern, Syst"},{"issue":"8","key":"pcbi.1014029.ref061","doi-asserted-by":"crossref","first-page":"5730","DOI":"10.1109\/TSMC.2025.3572738","article-title":"Link-Based Attributed Graph Clustering via Approximate Generative Bayesian Learning","volume":"55","author":"Y Yang","year":"2025","journal-title":"IEEE Trans Syst Man Cybern, Syst"},{"key":"pcbi.1014029.ref062","unstructured":"Kondor R, Pan H. The multiscale laplacian graph kernel. In: Advances in neural information processing systems, 2016."},{"issue":"4","key":"pcbi.1014029.ref063","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0284563","article-title":"Deep learning on graphs for multi-omics classification of COPD","volume":"18","author":"Y Zhuang","year":"2023","journal-title":"PLoS One"},{"key":"pcbi.1014029.ref064","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1007\/3-540-44581-1_27","article-title":"A Generalized Representer Theorem","author":"B Sch\u00f6lkopf","year":"2001","journal-title":"Lecture Notes in Computer Science"},{"issue":"1","key":"pcbi.1014029.ref065","article-title":"Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming","volume":"16","author":"JP Taylor-King","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1014029.ref066","volume-title":"Linear system theory and design","author":"CT Chen","year":"1984"},{"key":"pcbi.1014029.ref067","doi-asserted-by":"crossref","unstructured":"Preciado VM, Rahimian MA. Controllability Gramian spectra of random networks. In: 2016.","DOI":"10.1109\/ACC.2016.7525517"},{"key":"pcbi.1014029.ref068","unstructured":"Kazma MH, Taha AF. Observability for nonlinear systems: connecting variational dynamics, Lyapunov exponents, and empirical gramians. In: 2024. https:\/\/arxiv.org\/abs\/240214711"},{"issue":"4","key":"pcbi.1014029.ref069","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1007\/s00498-004-0141-4","article-title":"Gramian-Based Model Reduction for Descriptor Systems","volume":"16","author":"T Stykel","year":"2004","journal-title":"Mathematics of Control, Signals, and Systems (MCSS)"},{"key":"pcbi.1014029.ref070","doi-asserted-by":"crossref","DOI":"10.1117\/12.539387","article-title":"Model reduction based on modal Hankel singular values","volume-title":"Smart Structures and Materials 2004: Modeling, Signal Processing, and Control","author":"W Chang","year":"2004"},{"issue":"2","key":"pcbi.1014029.ref071","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1109\/TPWRD.2024.3364836","article-title":"Improved Pole Placement and Compaction of MIMO Vector Fitting Applied to System Identification","volume":"39","author":"AM Smith","year":"2024","journal-title":"IEEE Trans Power Delivery"},{"key":"pcbi.1014029.ref072","first-page":"1183","author":"MR Opmeer","year":"2015"},{"key":"pcbi.1014029.ref073","unstructured":"Kamiya S, Kitazono J, Oizumi M. Koopman Operator Based Dynamical Similarity Analysis for Data-driven Quantification of Distance between Dynamics. In: 2024."},{"key":"pcbi.1014029.ref074","author":"DA Haggerty","year":"2020"},{"issue":"5","key":"pcbi.1014029.ref075","first-page":"430","article-title":"The discrete Riccati equation of optimal control","volume":"8","author":"V Ku\u010dera","year":"1972","journal-title":"Kybernetika"},{"key":"pcbi.1014029.ref076","volume-title":"Model predictive control: theory, computation, and design","author":"JB Rawlings","year":"2017"},{"key":"pcbi.1014029.ref077","first-page":"67","article-title":"On the influence of the kernel on the consistency of support vector machines","volume":"2","author":"I Steinwart","year":"2001","journal-title":"J Mach Learn Res"},{"issue":"12","key":"pcbi.1014029.ref078","article-title":"Universal Kernels","volume":"7","author":"CA Micchelli","year":"2006","journal-title":"J Mach Learn Res"},{"key":"pcbi.1014029.ref079","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1515\/znc-1991-7-817","article-title":"Plant ADP-glucose pyrophosphorylase--recent advances and biotechnological perspectives (a review)","volume":"46","author":"LA Kleczkowski","year":"1991","journal-title":"Z Naturforsch C J Biosci"},{"issue":"4","key":"pcbi.1014029.ref080","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1007\/BF01816822","article-title":"Crassulacean acid metabolism in tropical dicotyledonous trees of the genusClusia","volume":"1","author":"M Popp","year":"1987","journal-title":"Trees"},{"issue":"5","key":"pcbi.1014029.ref081","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1111\/nph.17322","article-title":"Mesophyll-derived sugars are positive regulators of light-driven stomatal opening","volume":"230","author":"S Fl\u00fctsch","year":"2021","journal-title":"New Phytol"},{"key":"pcbi.1014029.ref082","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/j.plaphy.2019.12.020","article-title":"What does the RuBisCO activity tell us about a C3-CAM plant?","volume":"147","author":"AZ Goncalves","year":"2020","journal-title":"Plant Physiology and Biochemistry"},{"issue":"18","key":"pcbi.1014029.ref083","doi-asserted-by":"crossref","first-page":"108256","DOI":"10.1016\/j.jfranklin.2025.108256","article-title":"Control based on the Koopman operator: A comprehensive review","volume":"362","author":"JF Dur\u00e1n-Siguenza","year":"2025","journal-title":"Journal of the Franklin Institute"},{"issue":"6","key":"pcbi.1014029.ref084","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1109\/TAC.1971.1099819","article-title":"Controllability, observability, pole allocation, and state reconstruction","volume":"16","author":"J Willems","year":"1971","journal-title":"IEEE Trans Automat Contr"},{"issue":"1","key":"pcbi.1014029.ref085","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/s41598-017-00160-5","article-title":"Controllability and observability in complex networks - the effect of connection types","volume":"7","author":"D Leitold","year":"2017","journal-title":"Sci Rep"},{"issue":"4","key":"pcbi.1014029.ref086","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1104\/pp.103.037788","article-title":"The GATA family of transcription factors in Arabidopsis and rice","volume":"134","author":"JC Reyes","year":"2004","journal-title":"Plant Physiol"},{"issue":"2","key":"pcbi.1014029.ref087","doi-asserted-by":"crossref","first-page":"1419","DOI":"10.3390\/ijms24021419","article-title":"Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses","volume":"24","author":"Z-F Zuo","year":"2023","journal-title":"Int J Mol Sci"},{"key":"pcbi.1014029.ref088","first-page":"3599","article-title":"Temperature and pH responses of phosphofructokinase from three CAM plants, Ananas comosus, Kalancho\u00eb pinnata, and K. daigremontiana","author":"A Nose","year":"1998","journal-title":"Photosynthesis: Mechanisms and Effects"},{"issue":"6","key":"pcbi.1014029.ref089","doi-asserted-by":"crossref","first-page":"3497","DOI":"10.1016\/S0021-9258(19)39796-0","article-title":"Increased expression of a gene coding for NAD:glyceraldehyde-3-phosphate dehydrogenase during the transition from C3 photosynthesis to crassulacean acid metabolism in Mesembryanthemum crystallinum","volume":"265","author":"JA Ostrem","year":"1990","journal-title":"J Biol Chem"},{"key":"pcbi.1014029.ref090","doi-asserted-by":"crossref","first-page":"105145","DOI":"10.1016\/j.jprot.2024.105145","article-title":"Multiomics unravels potential molecular switches in the C3 to CAM transition of Mesembryanthemum crystallinum","volume":"299","author":"Q Guan","year":"2024","journal-title":"J Proteomics"},{"key":"pcbi.1014029.ref091","doi-asserted-by":"crossref","first-page":"104019","DOI":"10.1016\/j.jprot.2020.104019","article-title":"Comparative proteomics of Mesembryanthemum crystallinum guard cells and mesophyll cells in transition from C3 to CAM","volume":"231","author":"Q Guan","year":"2021","journal-title":"J Proteomics"},{"key":"pcbi.1014029.ref092","doi-asserted-by":"crossref","first-page":"154352","DOI":"10.1016\/j.jplph.2024.154352","article-title":"Sucrose synthase: An enzyme with multiple roles in plant physiology","volume":"303","author":"J Li","year":"2024","journal-title":"J Plant Physiol"},{"issue":"4","key":"pcbi.1014029.ref093","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1104\/pp.99.4.1275","article-title":"Role of sucrose-phosphate synthase in sucrose metabolism in leaves","volume":"99","author":"SC Huber","year":"1992","journal-title":"Plant Physiol"},{"issue":"4","key":"pcbi.1014029.ref094","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1007\/BF01816822","article-title":"Crassulacean acid metabolism in tropical dicotyledonous trees of the genusClusia","volume":"1","author":"M Popp","year":"1987","journal-title":"Trees"},{"key":"pcbi.1014029.ref095","doi-asserted-by":"crossref","first-page":"573197","DOI":"10.3389\/fpls.2020.573197","article-title":"Metabolic Modeling of the C3-CAM Continuum Revealed the Establishment of a Starch\/Sugar-Malate Cycle in CAM Evolution","volume":"11","author":"IYY Tay","year":"2021","journal-title":"Front Plant Sci"},{"issue":"1","key":"pcbi.1014029.ref096","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.gene.2013.04.022","article-title":"Emergence and expansion of TFIIB-like factors in the plant kingdom","volume":"526","author":"BA Knutson","year":"2013","journal-title":"Gene"},{"issue":"378","key":"pcbi.1014029.ref097","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1093\/jxb\/erf081","article-title":"CO(2)-concentrating: consequences in crassulacean acid metabolism","volume":"53","author":"U L\u00fcttge","year":"2002","journal-title":"J Exp Bot"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1014029","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T17:31:40Z","timestamp":1774978300000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1014029"}},"subtitle":[],"editor":[{"given":"Julio R.","family":"Banga","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,3,31]]},"references-count":97,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1014029","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,31]]}}}