{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:09:30Z","timestamp":1772172570981,"version":"3.50.1"},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2020,4,10]],"date-time":"2020-04-10T00:00:00Z","timestamp":1586476800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-0922391"],"award-info":[{"award-number":["DBI-0922391"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013904","name":"National Physical Science Consortium","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013904","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007197","type":"journal-article","created":{"date-parts":[[2020,4,10]],"date-time":"2020-04-10T13:25:07Z","timestamp":1586525107000},"page":"e1007197","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5513-9320","authenticated-orcid":true,"given":"Megan L.","family":"Matthews","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5392-0076","authenticated-orcid":true,"given":"Jack P.","family":"Wang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6819-7047","authenticated-orcid":true,"given":"Ronald","family":"Sederoff","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7152-9601","authenticated-orcid":true,"given":"Vincent L.","family":"Chiang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0477-9707","authenticated-orcid":true,"given":"Cranos M.","family":"Williams","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,4,10]]},"reference":[{"key":"pcbi.1007197.ref001","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/978-3-642-60469-0_4","volume-title":"Biochemistry and Molecular Biology of Wood","author":"T Higuchi","year":"1997"},{"issue":"3670","key":"pcbi.1007197.ref002","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1126\/science.148.3670.595","article-title":"Lignin: Its Constitution and Formation from p-Hydroxycinnamyl Alcohols","volume":"148","author":"K Freudenberg","year":"1965","journal-title":"Science"},{"issue":"1","key":"pcbi.1007197.ref003","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1146\/annurev.py.18.090180.001355","article-title":"Lignification as a Mechanism of Disease Resistance","volume":"18","author":"CP Vance","year":"1980","journal-title":"Annual Review of Phytopathology"},{"issue":"1","key":"pcbi.1007197.ref004","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1038\/s41467-018-03863-z","article-title":"Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis","volume":"9","author":"JP Wang","year":"2018","journal-title":"Nature Communications"},{"key":"pcbi.1007197.ref005","first-page":"95","article-title":"Precursors and their polymerization","author":"KV Sarkanen","year":"1971","journal-title":"Lignins: occurrence, formation, structure and reactions"},{"issue":"49","key":"pcbi.1007197.ref006","doi-asserted-by":"crossref","first-page":"21199","DOI":"10.1073\/pnas.1007431107","article-title":"Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana","volume":"107","author":"Y Li","year":"2010","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"pcbi.1007197.ref007","doi-asserted-by":"crossref","first-page":"1346","DOI":"10.1111\/nph.14220","article-title":"Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping","volume":"213","author":"MPM Thoen","year":"2017","journal-title":"New Phytologist"},{"issue":"2","key":"pcbi.1007197.ref008","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/hdy.2008.76","article-title":"Genetics of phenotypic plasticity: QTL analysis in barley, Hordeum vulgare","volume":"102","author":"X Lacaze","year":"2009","journal-title":"Heredity"},{"issue":"8","key":"pcbi.1007197.ref009","doi-asserted-by":"crossref","first-page":"e103997","DOI":"10.1371\/journal.pone.0103997","article-title":"A New Method to Infer Causal Phenotype Networks Using QTL and Phenotypic Information","volume":"9","author":"H Wang","year":"2014","journal-title":"PLoS ONE"},{"key":"pcbi.1007197.ref010","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.3389\/fpls.2017.01564","article-title":"Multilevel Regulation of Abiotic Stress Responses in Plants","volume":"8","author":"DC Haak","year":"2017","journal-title":"Frontiers in Plant Science"},{"issue":"1","key":"pcbi.1007197.ref011","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1104\/pp.108.129791","article-title":"Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses","volume":"149","author":"K Nakashima","year":"2009","journal-title":"Plant physiology"},{"key":"pcbi.1007197.ref012","article-title":"Hierarchical Transcription-Factor and Chromatin Binding Network for Wood Formation in Populus trichocarpa","author":"H Chen","year":"2019","journal-title":"The Plant cell"},{"issue":"4","key":"pcbi.1007197.ref013","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nrg3185","article-title":"Insights into the regulation of protein abundance from proteomic and transcriptomic analyses","volume":"13","author":"C Vogel","year":"2012","journal-title":"Nature Reviews Genetics"},{"issue":"3","key":"pcbi.1007197.ref014","first-page":"15017","article-title":"Protein turnover in plant biology","volume":"1","author":"CJ Nelson","year":"2015","journal-title":"Nature Plants 2015 1:3"},{"issue":"27","key":"pcbi.1007197.ref015","doi-asserted-by":"crossref","first-page":"8481","DOI":"10.1073\/pnas.1510473112","article-title":"Phosphorylation is an on\/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis","volume":"112","author":"JP Wang","year":"2015","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"2","key":"pcbi.1007197.ref016","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1007\/s00216-016-9776-5","article-title":"N-linked glycosite profiling and use of Skyline as a platform for characterization and relative quantification of glycans in differentiating xylem of Populus trichocarpa","volume":"409","author":"PL Loziuk","year":"2017","journal-title":"Analytical and Bioanalytical Chemistry"},{"issue":"1","key":"pcbi.1007197.ref017","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.molp.2014.12.003","article-title":"4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid:Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa","volume":"8","author":"CY Lin","year":"2015","journal-title":"Molecular Plant"},{"issue":"3","key":"pcbi.1007197.ref018","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1105\/tpc.113.120881","article-title":"Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin in Populus trichocarpa","volume":"26","author":"JP Wang","year":"2014","journal-title":"The Plant Cell"},{"issue":"1","key":"pcbi.1007197.ref019","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1186\/1471-2164-10-505","article-title":"Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics","volume":"10","author":"E Jamet","year":"2009","journal-title":"BMC Genomics"},{"issue":"1","key":"pcbi.1007197.ref020","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1471-2229-9-6","article-title":"Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes","volume":"9","author":"Z Minic","year":"2009","journal-title":"BMC Plant Biology"},{"issue":"1","key":"pcbi.1007197.ref021","doi-asserted-by":"crossref","first-page":"31","DOI":"10.5511\/plantbiotechnology.18.0129a","article-title":"Proteomic analysis of xylem vessel cell differentiation in VND7-inducible tobacco BY-2 cells by two-dimensional gel electrophoresis","volume":"35","author":"M Noguchi","year":"2018","journal-title":"Plant Biotechnology"},{"issue":"3-4","key":"pcbi.1007197.ref022","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1089\/106652700750050961","article-title":"Using Bayesian Networks to Analyze Expression Data","volume":"7","author":"N Friedman","year":"2000","journal-title":"Journal of Computational Biology"},{"issue":"2-3","key":"pcbi.1007197.ref023","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.biosystems.2006.09.026","article-title":"Bayesian learning of sparse gene regulatory networks","volume":"87","author":"ZSH Chan","year":"2007","journal-title":"Biosystems"},{"issue":"8","key":"pcbi.1007197.ref024","doi-asserted-by":"crossref","first-page":"e1005024","DOI":"10.1371\/journal.pcbi.1005024","article-title":"Inference of Gene Regulatory Network Based on Local Bayesian Networks","volume":"12","author":"F Liu","year":"2016","journal-title":"PLOS Computational Biology"},{"issue":"2","key":"pcbi.1007197.ref025","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1002\/bimj.200800185","article-title":"Nested effects models for learning signaling networks from perturbation data","volume":"51","author":"H Fr\u00f6hlich","year":"2009","journal-title":"Biometrical Journal"},{"issue":"2","key":"pcbi.1007197.ref026","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1093\/bioinformatics\/btq631","article-title":"Fast and efficient dynamic nested effects models","volume":"27","author":"H Fr\u00f6hlich","year":"2011","journal-title":"Bioinformatics"},{"issue":"12","key":"pcbi.1007197.ref027","doi-asserted-by":"crossref","first-page":"e1001014","DOI":"10.1371\/journal.pcbi.1001014","article-title":"Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations","volume":"6","author":"BA Logsdon","year":"2010","journal-title":"PLoS Computational Biology"},{"issue":"5","key":"pcbi.1007197.ref028","doi-asserted-by":"crossref","first-page":"e1003068","DOI":"10.1371\/journal.pcbi.1003068","article-title":"Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations","volume":"9","author":"X Cai","year":"2013","journal-title":"PLoS Computational Biology"},{"issue":"6","key":"pcbi.1007197.ref029","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1038\/nbt0602-557","article-title":"From rags to riches","volume":"20","author":"VL Chiang","year":"2002","journal-title":"Nature Biotechnology"},{"issue":"7","key":"pcbi.1007197.ref030","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/nbt1316","article-title":"Lignin modification improves fermentable sugar yields for biofuel production","volume":"25","author":"F Chen","year":"2007","journal-title":"Nature Biotechnology"},{"issue":"1","key":"pcbi.1007197.ref031","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.mbs.2010.08.009","article-title":"Mathematical modeling of monolignol biosynthesis in Populus xylem","volume":"228","author":"Y Lee","year":"2010","journal-title":"Mathematical Biosciences"},{"issue":"1","key":"pcbi.1007197.ref032","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/s13068-015-0334-8","article-title":"Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum","volume":"8","author":"M Faraji","year":"2015","journal-title":"Biotechnology for Biofuels"},{"issue":"4","key":"pcbi.1007197.ref033","doi-asserted-by":"crossref","first-page":"61","DOI":"10.3390\/pr5040061","article-title":"Improving Bioenergy Crops through Dynamic Metabolic Modeling","volume":"5","author":"M Faraji","year":"2017","journal-title":"Processes"},{"issue":"1","key":"pcbi.1007197.ref034","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1186\/s13068-018-1241-6","article-title":"A dynamic model of lignin biosynthesis in Brachypodium distachyon","volume":"11","author":"M Faraji","year":"2018","journal-title":"Biotechnology for Biofuels"},{"issue":"6","key":"pcbi.1007197.ref035","doi-asserted-by":"crossref","first-page":"3390","DOI":"10.1021\/pr300205a","article-title":"Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry","volume":"11","author":"CM Shuford","year":"2012","journal-title":"Journal of Proteome Research"},{"issue":"12","key":"pcbi.1007197.ref036","doi-asserted-by":"crossref","first-page":"4081","DOI":"10.1016\/0031-9422(92)80418-E","article-title":"A role for phosphorylation in the down-regulation of phenylalanine ammonia-lyase in suspension-cultured cells of french bean","volume":"31","author":"GP Bolwell","year":"1992","journal-title":"Phytochemistry"},{"issue":"1","key":"pcbi.1007197.ref037","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/S0014-5793(99)00998-9","article-title":"Phosphorylation of phenylalanine ammonia-lyase: evidence for a novel protein kinase and identification of the phosphorylated residue","volume":"457","author":"EG Allwood","year":"1999","journal-title":"FEBS Letters"},{"issue":"12","key":"pcbi.1007197.ref038","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biology"},{"issue":"7","key":"pcbi.1007197.ref039","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"ME Ritchie","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"pcbi.1007197.ref040","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1214\/16-AOAS920","article-title":"Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression","volume":"10","author":"B Phipson","year":"2016","journal-title":"The annals of applied statistics"},{"key":"pcbi.1007197.ref041","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.euprot.2015.02.002","article-title":"Detecting significant changes in protein abundance","volume":"7","author":"K Kammers","year":"2015","journal-title":"EuPA Open Proteomics"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007197","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,4,10]],"date-time":"2020-04-10T13:25:53Z","timestamp":1586525153000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007197"}},"subtitle":[],"editor":[{"given":"Sushmita","family":"Roy","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,4,10]]},"references-count":41,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2020,4,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007197","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/677047","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,10]]}}}