Researcher Profile

Researcher Profile

Rongling Wu, PhD

Rongling Wu, PhD

Distinguished Professor, Department of Public Health Sciences
Division of Biostatistics and Bioinformatics
Director, Center for Statistical Genetics
Scientific Program:Cancer Control
rxw35@psu.edu

Research Interests

  • Quantitative Trait Loci
  • Genes
  • Growth
  • Population
  • Statistical Models
  • Populus
  • Genome
  • Genotype
  • Chromosome Mapping
  • Single Nucleotide Polymorphism
  • Phenotype
  • Pharmaceutical Preparations

Recent Publications

2019

Sang, M, Shi, H, Wei, K, Ye, M, Jiang, L, Sun, L & Wu, R 2019, 'A dissection model for mapping complex traits' Plant Journal, vol. 97, no. 6, pp. 1168-1182. https://doi.org/10.1111/tpj.14185
Zeng, Y, Zhu, X, Chen, C, Banerjee, K, Sun, L, Yu, W, Zheng, B & Wu, R 2019, 'A unified DNA sequence and non-DNA sequence mapping model of complex traits', Plant Journal. https://doi.org/10.1111/tpj.14354
Wang, Q, Gan, J, Wei, K, Berceli, SA, Gragnoli, C & Wu, R 2019, 'A unified mapping framework of multifaceted pharmacodynamic responses to hypertension interventions', Drug Discovery Today, vol. 24, no. 3, pp. 883-889. https://doi.org/10.1016/j.drudis.2019.01.009
Banerjee, K, Zhao, N, Srinivasan, A, Xue, L, Hicks, S, Middleton, FA, Wu, R & Zhan, X 2019, 'An adaptive multivariate two-sample test with application to microbiome differential abundance analysis', Frontiers in Genetics, vol. 10, no. APR, 350. https://doi.org/10.3389/fgene.2019.00350
Postolache, TT, del Bosque-Plata, L, Jabbour, S, Vergare, M, Wu, R & Gragnoli, C 2019, 'Co-shared genetics and possible risk gene pathway partially explain the comorbidity of schizophrenia, major depressive disorder, type 2 diabetes, and metabolic syndrome', American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics, vol. 180, no. 3, pp. 186-203. https://doi.org/10.1002/ajmg.b.32712
Jiang, L, Sun, L, Ye, M, Wang, J, Wang, Y, Bogard, M, Lacaze, X, Fournier, A, Beauchêne, K, Gouache, D & Wu, R 2019, 'Functional mapping of N deficiency-induced response in wheat yield-component traits by implementing high-throughput phenotyping', Plant Journal, vol. 97, no. 6, pp. 1105-1119. https://doi.org/10.1111/tpj.14186
Gan, J, Cao, Y, Jiang, L & Wu, R 2019, 'Mapping covariation quantitative trait loci that control organ growth and whole-plant biomass', Frontiers in Plant Science, vol. 10, 719. https://doi.org/10.3389/fpls.2019.00719
Wang, P, Jiang, L, Ye, M, Zhu, X & Wu, R 2019, 'The genomic landscape of crossover interference in the desert tree populus euphratica', Frontiers in Genetics, vol. 10, no. MAY, 440. https://doi.org/10.3389/fgene.2019.00440
Ye, M, Jiang, L, Chen, C, Zhu, X, Wang, M & Wu, R 2019, 'np2QTL: networking phenotypic plasticity quantitative trait loci across heterogeneous environments' the Plant Journal. https://doi.org/10.1111/tpj.14355
Ye, M, Jiang, L, Chen, C, Zhu, X, Wang, M & Wu, R 2019, 'np2QTL: networking phenotypic plasticity quantitative trait loci across heterogeneous environments', Plant Journal. https://doi.org/10.1111/tpj.14355

2018

Jiang, L, Shi, C, Ye, M, Xi, F, Cao, Y, Wang, L, Zhang, M, Sang, M & Wu, R 2018, 'A computational-experimental framework for mapping plant coexistence', Methods in Ecology and Evolution, vol. 9, no. 5, pp. 1335-1352. https://doi.org/10.1111/2041-210X.12981
Jiang, L, He, X, Jin, Y, Ye, M, Sang, M, Chen, N, Zhu, J, Zhang, Z, Li, J & Wu, R 2018, 'A mapping framework of competition–cooperation QTLs that drive community dynamics', Nature communications, vol. 9, no. 1, 3010. https://doi.org/10.1038/s41467-018-05416-w
Wei, K, Wang, J, Sang, M, Zhang, S, Zhou, H, Jiang, L, Clavijo Michelangeli, JA, Vallejos, CE & Wu, R 2018, 'An ecophysiologically based mapping model identifies a major pleiotropic QTL for leaf growth trajectories of Phaseolus vulgaris' Plant Journal, vol. 95, no. 5, pp. 775-784. https://doi.org/10.1111/tpj.13986
Gosik, K, Sun, L, Chinchilli, V & Wu, R 2018, 'An ultrahigh-dimensional mapping model of high-order epistatic networks for complex traits' Current Genomics, vol. 19, no. 5, pp. 384-394. https://doi.org/10.2174/1389202919666171218162210
Gragnoli, C, Wu, R & Ahmed, I 2018, 'Breastfeeding and future maternal health- no causal evidence: To the editor' JAMA Internal Medicine, vol. 178, no. 6, pp. 869-870. https://doi.org/10.1001/jamainternmed.2018.1806
Wang, Z, Song, S, Sheng, S, Tian, J, Wu, R & Pang, X 2018, 'Comparative transcriptome analysis identifies differentially expressed genes between normal and late-blooming Siberian apricot' Journal of Forestry Research. https://doi.org/10.1007/s11676-018-0825-0
Zhao, G, Fu, Y, Su, Z & Wu, R 2018, 'How Long Non-Coding RNAs and MicroRNAs Mediate the Endogenous RNA Network of Head and Neck Squamous Cell Carcinoma: A Comprehensive Analysis', Cellular Physiology and Biochemistry, vol. 50, no. 1, pp. 342-352. https://doi.org/10.1159/000494009
Fu, L, Sun, L, Hao, H, Jiang, L, Zhu, S, Ye, M, Tang, S, Huang, M & Wu, R 2018, 'How trees allocate carbon for optimal growth: insight from a game-theoretic model', Briefings in bioinformatics, vol. 19, no. 4, pp. 593-602. https://doi.org/10.1093/bib/bbx003
Sun, L, Wang, J, Zhu, X, Jiang, L, Gosik, K, Sang, M, Sun, F, Cheng, T, Zhang, Q & Wu, R 2018, 'HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly' Briefings in bioinformatics, vol. 19, no. 4, pp. 603-612. https://doi.org/10.1093/bib/bbx011
Rehfuss, JP, DeSart, KM, Rozowsky, JM, O'Malley, KA, Moldawer, LL, Baker, HV, Wang, Y, Wu, R, Nelson, PR & Berceli, SA 2018, 'Hyperacute Monocyte Gene Response Patterns Are Associated With Lower Extremity Vein Bypass Graft Failure' Circulation. Genomic and precision medicine, vol. 11, no. 3, pp. e001970. https://doi.org/10.1161/CIRCGEN.117.001970
Wei, K, Wang, Q, Gan, J, Zhang, S, Ye, M, Gragnoli, C & Wu, R 2018, 'Mapping genes for drug chronotherapy', Drug Discovery Today, vol. 23, no. 11, pp. 1883-1888. https://doi.org/10.1016/j.drudis.2018.06.011
Fu, G, Huang, M, Bo, W, Hao, H & Wu, R 2018, 'Mapping morphological shape as a high-dimensional functional curve' Briefings in bioinformatics, vol. 19, no. 3, pp. 461-471. https://doi.org/10.1093/bib/bbw111
Wen, YJ, Zhang, H, Ni, YL, Huang, B, Zhang, J, Feng, JY, Wang, SB, Dunwell, JM, Zhang, YM & Wu, R 2018, 'Methodological implementation of mixed linear models in multi-locus genome-wide association studies', Briefings in bioinformatics, vol. 19, no. 4, pp. 700-712. https://doi.org/10.1093/bib/bbw145
Zhang, Q, Zhang, H, Sun, L, Fan, G, Ye, M, Jiang, L, Liu, X, Ma, K, Shi, C, Bao, F, Guan, R, Han, Y, Fu, Y, Pan, H, Chen, Z, Li, L, Wang, J, Lv, M, Zheng, T, Yuan, C, Zhou, Y, Lee, SMY, Yan, X, Xu, X, Wu, R, Chen, W & Cheng, T 2018, 'The genetic architecture of floral traits in the woody plant Prunus mume', Nature communications, vol. 9, no. 1, 1702. https://doi.org/10.1038/s41467-018-04093-z
Liu, J, Ye, M, Zhu, S, Jiang, L, Sang, M, Gan, J, Wang, Q, Huang, M & Wu, R 2018, 'Two-stage identification of SNP effects on dynamic poplar growth', Plant Journal, vol. 93, no. 2, pp. 286-296. https://doi.org/10.1111/tpj.13777
Wang, Z, Wang, N, Wu, R & Wang, Z 2018, 'fGWAS: An R package for genome-wide association analysis with longitudinal phenotypes', Journal of Genetics and Genomics, vol. 45, no. 7, pp. 411-413. https://doi.org/10.1016/j.jgg.2018.06.006
Wang, P, Wang, D, Wang, J, Jiang, L & Wu, R 2018, '胡杨幼苗生长相关性状QTL上位性分析' Beijing Linye Daxue Xuebao/Journal of Beijing Forestry University, vol. 40, no. 12, pp. 49-59. https://doi.org/10.13332/j.1000-1522.20180332

2017

Yan, Q, Zhu, X, Jiang, L, Ye, M, Sun, L, Terblanche, JS & Wu, R 2017, 'A computing platform to map ecological metabolism by integrating functional mapping and the metabolic theory of ecology' Briefings in Bioinformatics, vol. 18, no. 1, pp. 137-144. https://doi.org/10.1093/bib/bbv116
Wang, J, Sun, L, Jiang, L, Sang, M, Ye, M, Cheng, T, Zhang, Q & Wu, R 2017, 'A high-dimensional linkage analysis model for characterizing crossover interference', Briefings in bioinformatics, vol. 18, no. 3, pp. 382-393. https://doi.org/10.1093/bib/bbw033
Hao, H, Sun, L, Zhu, X & Wu, R 2017, 'A nonparametric approach for functional mapping of complex traits' Statistics and its Interface, vol. 10, no. 3, pp. 387-397. https://doi.org/10.4310/SII.2017.v10.n3.a3
Zhu, X, Li, H, Ye, M, Jiang, L, Sang, M & Wu, R 2017, 'AlloMap6: An R package for genetic linkage analysis in allohexaploids', Briefings in bioinformatics, vol. 18, no. 6, pp. 919-927. https://doi.org/10.1093/bib/bbw085
Lin, Z, Hao, H, Hegarty, JP, Lin, TR, Wang, Y, Harris, LR, Xu, HN, Wu, R, Thomas, N & Floros, J 2017, 'Association of the haem oxygenase-1 gene with inflammatory bowel disease', Swiss Medical Weekly, vol. 147, w14456. https://doi.org/10.4414/smw.2017.14456
He, X, Jin, Y, Ye, M, Chen, N, Zhu, J, Wang, J, Jiang, L & Wu, R 2017, 'Bacterial genetic architecture of ecological interactions in co-culture by GWAS-taking Escherichia coli and Staphylococcus aureus as an example' Frontiers in Microbiology, vol. 8, no. NOV, 2332. https://doi.org/10.3389/fmicb.2017.02332
Jiang, L, Zhang, M, Sang, M, Ye, M & Wu, R 2017, 'Evo-Devo-EpiR: a genome-wide search platform for epistatic control on the evolution of development', Briefings in bioinformatics, vol. 18, no. 5, pp. 754-760. https://doi.org/10.1093/bib/bbw062
Lin, Z, Wang, Z, Hegarty, JP, Lin, TR, Wang, Y, Deiling, S, Wu, R, Thomas, N & Floros, J 2017, 'Genetic association and epistatic interaction of the interleukin-10 signaling pathway in pediatric inflammatory bowel disease', World Journal of Gastroenterology, vol. 23, no. 27, pp. 4897-4909. https://doi.org/10.3748/wjg.v23.i27.4897
Wang, Q, Gosik, K, Xing, S, Jiang, L, Sun, L, Chinchilli, V & Wu, R 2017, 'Integration of epigenetic game theory and developmental principles: Reply to comments on “Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition”' Physics of Life Reviews, vol. 20, pp. 166-169. https://doi.org/10.1016/j.plrev.2017.01.029
Sun, L, Wang, J, Sang, M, Jiang, L, Zhao, B, Cheng, T, Zhang, Q & Wu, R 2017, 'Landscaping Crossover Interference Across a Genome', Trends in Plant Science, vol. 22, no. 10, pp. 894-907. https://doi.org/10.1016/j.tplants.2017.06.008
Gao, P, Cui, YL & Wu, R 2018, 'Molecular dynamic modeling of CYP51B in complex with azole inhibitors', Journal of Biomolecular Structure and Dynamics, vol. 36, no. 6, pp. 1511-1519. https://doi.org/10.1080/07391102.2017.1328315
Cui, YL & Wu, R 2017, 'Molecular dynamics investigations of membrane-bound CYP2C19 polymorphisms reveal distinct mechanisms for peripheral variants by long-range effects on the enzymatic activity', Molecular BioSystems, vol. 13, no. 6, pp. 1070-1079. https://doi.org/10.1039/c6mb00827e
Wang, Y, Li, X, Jiang, L, Han, W, Xie, X, Jin, Y, He, X & Wu, R 2017, 'Novel mutation sites in the development of vancomycin- intermediate resistance in staphylococcus aureus', Frontiers in Microbiology, vol. 7, no. JAN, 2163. https://doi.org/10.3389/fmicb.2016.02163
Wang, Z, Zeng, Y, Zhang, Z, Sheng, S, Tian, J, Wu, R & Pang, X 2017, 'Phylogeography study of the siberian apricot (Prunus sibirica L.) in Northern China assessed by chloroplast microsatellite and DNA makers', Frontiers in Plant Science, vol. 8, 1989. https://doi.org/10.3389/fpls.2017.01989
Zhang, J, Yuan, H, Yang, Q, Li, M, Wang, Y, Li, Y, Ma, X, Tan, F & Wu, R 2017, 'The genetic architecture of growth traits in Salix matsudana under salt stress', Horticulture Research, vol. 4, 17024. https://doi.org/10.1038/hortres.2017.24
Sun, L, Sang, M, Zheng, C, Wang, D, Shi, H, Liu, K, Guo, Y, Cheng, T, Zhang, Q & Wu, R 2017, 'The genetic architecture of heterochrony as a quantitative trait: Lessons from a computational model', Briefings in bioinformatics, vol. 19, no. 6, pp. 1430-1439. https://doi.org/10.1093/bib/bbx056
Zhang, M, Bo, W, Xu, F, Li, H, Ye, M, Jiang, L, Shi, C, Fu, Y, Zhao, G, Huang, Y, Gosik, K, Liang, D & Wu, R 2017, 'The genetic architecture of shoot–root covariation during seedling emergence of a desert tree, Populus euphratica', Plant Journal, vol. 90, no. 5, pp. 918-928. https://doi.org/10.1111/tpj.13518
Wang, L, Wu, R & Bo, W 2018, 'Transcriptome profiling of PeCRY1 transgenic Populus tomentosa' Genes and Genomics, vol. 40, no. 4, pp. 349-359. https://doi.org/10.1007/s13258-017-0631-7
Gosik, K, Kong, L, Chinchilli, V & Wu, R 2017, 'iFORM/eQTL: An ultrahigh-dimensional platform for inferring the global genetic architecture of gene transcripts', Briefings in Bioinformatics, vol. 18, no. 2, pp. 250-259. https://doi.org/10.1093/bib/bbw014

2016

Wang, N, Gosik, K, Li, R, Lindsay, B & Wu, R 2016, 'A block mixture model to map eQTLs for gene clustering and networking' Scientific reports, vol. 6, 21193. https://doi.org/10.1038/srep21193
Xu, M, Jiang, L, Zhu, S, Zhou, C, Ye, M, Mao, K, Sun, L, Su, X, Pan, H, Zhang, S, Huang, M & Wu, R 2016, 'A computational framework for mapping the timing of vegetative phase change', The New phytologist, vol. 211, no. 2, pp. 750-760. https://doi.org/10.1111/nph.13907
Zhang, J, Yuan, H, Li, M, Li, Y, Wang, Y, Ma, X, Zhang, Y, Tan, F & Wu, R 2016, 'A high-density genetic map of tetraploid salix matsudana using specific length amplified fragment sequencing (SLAF-seq)', PLoS One, vol. 11, no. 6, e0157777. https://doi.org/10.1371/journal.pone.0157777
Jiang, L, Ye, M, Zhu, S, Zhai, Y, Xu, M, Huang, M & Wu, R 2016, 'Computational identification of genes modulating stem height–diameter allometry', Plant Biotechnology Journal, vol. 14, no. 12, pp. 2254-2264. https://doi.org/10.1111/pbi.12579
Wang, Q, Gosik, K, Xing, S, Jiang, L, Sun, L, Chinchilli, V & Wu, R 2017, 'Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition', Physics of Life Reviews, vol. 20, pp. 126-137. https://doi.org/10.1016/j.plrev.2016.11.001
Cao, J, Wang, L, Huang, Z, Gai, J & Wu, R 2017, 'Functional Mapping of Multiple Dynamic Traits', Journal of Agricultural, Biological, and Environmental Statistics, vol. 22, no. 1, pp. 60-75. https://doi.org/10.1007/s13253-016-0275-0
Zhu, X, Jiang, L, Ye, M, Sun, L, Gragnoli, C & Wu, R 2016, 'Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping', Trends in Genetics, vol. 32, no. 5, pp. 256-268. https://doi.org/10.1016/j.tig.2016.02.004
Cui, YL, Xu, F & Wu, R 2016, 'Molecular dynamics investigations of regioselectivity of anionic/aromatic substrates by a family of enzymes a case study of diclofenac binding in CYP2C isoforms' Physical Chemistry Chemical Physics, vol. 18, no. 26, pp. 17428-17439. https://doi.org/10.1039/c6cp01128d
Wang, J, Jiang, L & Wu, R 2017, 'Plant grafting: how genetic exchange promotes vascular reconnection', New Phytologist, vol. 214, no. 1, pp. 56-65. https://doi.org/10.1111/nph.14383
Luo, J, Berg, A, Ahn, K, Das, K, Li, J, Wang, Z, Li, Y & Wu, R 2016, [No title available]. in Handbook of Adaptive Designs in Pharmaceutical and Clinical Development. CRC Press.

2015

Jiang, L, Liu, J, Zhu, X, Ye, M, Sun, L, Lacaze, X & Wu, R 2015, '2HiGWAS: A unifying high-dimensional platform to infer the global genetic architecture of trait development', Briefings in bioinformatics, vol. 16, no. 6, bbv002, pp. 905-911. https://doi.org/10.1093/bib/bbv002
Ye, M, Wang, Z, Wang, Y & Wu, R 2015, 'A multi-Poisson dynamic mixture model to cluster developmental patterns of gene expression by RNA-seq' Briefings in bioinformatics, vol. 16, no. 2, bbu013, pp. 205-215. https://doi.org/10.1093/bib/bbu013
Yin, D, Zhu, X, Jiang, L, Zhang, J, Zeng, Y & Wu, R 2015, 'A reciprocal cross design to map the genetic architecture of complex traits in apomictic plants', New Phytologist, vol. 205, no. 3, pp. 1360-1367. https://doi.org/10.1111/nph.13128
Sun, L, Zhu, X, Zhang, Q & Wu, R 2015, 'A unifying experimental design for dissecting tree genomes', Trends in Plant Science, vol. 20, no. 8, pp. 473-476. https://doi.org/10.1016/j.tplants.2015.05.012
Si, J, Zhao, R & Wu, R 2015, 'An overview of the prediction of protein DNA-binding sites', International journal of molecular sciences, vol. 16, no. 3, pp. 5194-5215. https://doi.org/10.3390/ijms16035194
Li, J, Wang, Z, Li, R & Wu, R 2015, 'Bayesian group lasso for nonparametric varying-coefficient models with application to functional genome-wide association studies', Annals of Applied Statistics, vol. 9, no. 2, pp. 640-664. https://doi.org/10.1214/15-AOAS808
Si, J, Cui, J, Cheng, J & Wu, R 2015, 'Computational prediction of RNA-binding proteins and binding sites', International journal of molecular sciences, vol. 16, no. 11, pp. 26303-26317. https://doi.org/10.3390/ijms161125952
Zhu, X, Dong, L, Jiang, L, Li, H, Sun, L, Zhang, H, Yu, W, Liu, H, Dai, W, Zeng, Y & Wu, R 2015, 'Constructing a linkage-linkage disequilibrium map using dominant-segregating markers', DNA Research, vol. 23, no. 1, pp. 1-10. https://doi.org/10.1093/dnares/dsv031
Sun, L, Jiang, L, Ye, M, Zhu, X, Wang, J, Gosik, K & Wu, R 2015, Functional mapping: How to map genes for phenotypic plasticity of development. in Evolutionary Biology: Biodiversification from Genotype to Phenotype. Springer International Publishing, pp. 3-17. https://doi.org/10.1007/978-3-319-19932-0_1
SHARP Investigators 2015, 'Genome-wide association study of short-acting β2-agonists a novel genome-wide significant locus on chromosome 2 near ASB3', American journal of respiratory and critical care medicine, vol. 191, no. 5, pp. 530-537. https://doi.org/10.1164/rccm.201408-1426OC
Zhu, X, Xu, F, Zhao, S, Bo, W, Jiang, L, Pang, X & Wu, R 2015, 'Inferring the evolutionary history of outcrossing populations through computing a multiallelic linkage-linkage disequilibrium map', Methods in Ecology and Evolution, vol. 6, no. 11, pp. 1259-1269. https://doi.org/10.1111/2041-210X.12428
Sun, L & Wu, R 2015, 'Mapping complex traits as a dynamic system', Physics of Life Reviews, vol. 13, pp. 155-185. https://doi.org/10.1016/j.plrev.2015.02.007
Mao, K, Wang, L, Li, YY & Wu, R 2015, 'Molecular cloning and functional analysis of UV RESISTANCE LOCUS 8 (PeUVR8) from Populus euphratica', PloS one, vol. 10, no. 7, e0132390. https://doi.org/10.1371/journal.pone.0132390
Wang, Y, Tong, C, Wang, Z, Wang, Z, Mauger, D, Tantisira, KG, Israel, E, Szefler, SJ, Chinchilli, V, Boushey, HA, Lazarus, SC, Lemanske, RF & Wu, R 2015, 'Pharmacodynamic genome-wide association study identifies new responsive loci for glucocorticoid intervention in asthma' Pharmacogenomics Journal, vol. 15, no. 5, pp. 422-429. https://doi.org/10.1038/tpj.2014.83
Jiang, L, Clavijo, JA, Sun, L, Zhu, X, Bhakta, MS, Gezan, SA, Carvalho, M, Vallejos, CE & Wu, R 2015, 'Plastic expression of heterochrony quantitative trait loci (hQTLs) for leaf growth in the common bean (Phaseolus vulgaris)', New Phytologist, vol. 207, no. 3, pp. 872-882. https://doi.org/10.1111/nph.13386
Si, J, Zhao, X, Zhao, X & Wu, R 2015, 'Systematic functional genomics resource and annotation for poplar' IET Systems Biology, vol. 9, no. 4, pp. 164-171. https://doi.org/10.1049/iet-syb.2014.0047
Zhou, L, Shen, Y, Jiang, L, Yin, D, Guo, J, Zheng, H, Sun, H, Wu, R & Guo, Y 2015, 'Systems mapping for hematopoietic progenitor cell heterogeneity' PloS one, vol. 10, no. 5, e0126937. https://doi.org/10.1371/journal.pone.0126937
Hao, H, Haas, MJ, Wu, R & Gragnoli, C 2015, 'T2D and Depression Risk Gene Proteasome Modulator 9 is Linked to Insomnia' Scientific reports, vol. 5, 12032. https://doi.org/10.1038/srep12032
Sun, L & Wu, R 2015, 'Toward the practical utility of systems mapping. Reply to comments on "Mapping complex traits as a dynamic system"' Physics of Life Reviews, vol. 13, pp. 198-201. https://doi.org/10.1016/j.plrev.2015.04.038

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