المؤلفون: Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi, Bo Zheng

المصدر: BMC Genomics, Vol 21, Iss 1, Pp 1-17 (2020)

مصطلحات موضوعية: Peptide hormone, CLE, Machine learning, Euclidean distance, Gene prediction, Gene clustering, Biotechnology, TP248.13-248.65, Genetics, QH426-470

وصف الملف: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-020-07114-8; https://doaj.org/toc/1471-2164

URL الوصول: https://doaj.org/article/8e7126b67a6040a88897a0deae9d6ed4

المؤلفون: Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi, Bo Zheng

المصدر: BMC Genomics, Vol 21, Iss 1, Pp 1-2 (2020)

مصطلحات موضوعية: Biotechnology, TP248.13-248.65, Genetics, QH426-470

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1471-2164

URL الوصول: https://doaj.org/article/8b8be2f5529f4e53b7fa270c2e8e7e72

المؤلفون: Eswaran, Gugan, Zhang, Xixi, Rutten, Jacob Pieter, Han, Jingyi, Iida, Hiroyuki, López Ortiz, Jennifer, Mäkilä, Riikka, Wybouw, Brecht, Jiménez, Benjamin Planterose, Vainio, Leo, Porcher, Alexis, Gavarron, Marina Leal, Zhang, Jing, Blomster, Tiina, Wang, Xin, Dolan, David, Smetana, Ondřej, Brady, Siobhán M., Topcu, Melis Kucukoglu, Tusscher, Kirsten ten, Etchells, J. Peter, Mähönen, Ari Pekka

المساهمون: Organismal and Evolutionary Biology Research Programme, Helsinki Institute of Life Science HiLIFE, Institute of Biotechnology, University of Helsinki, Institute of Biotechnology (-2009), Doctoral Programme in Plant Sciences, Crop Light, Viikki Plant Science Centre (ViPS), Ari Pekka Mähönen / Principal Investigator, Plant Biology

مصطلحات موضوعية: 11831 Plant biology, Arabidopsis root, Secondary growth, Wood formation, Cle peptides, Gene, Diffusion, Aintegumenta, Proteins, Wall, Pxy

وصف الملف: application/pdf

Relation: We thank V. Willemsen, K. Prasad, and B. Krizek for providing published material and J. Traas for providing the unpublished entry clone containing the AIL6/PLT3 promoter; J. Vainonen for help with protein work; and Y. Helariutta for providing feedback on the manuscript. We acknowledge support for RNA-seq from DNA Sequencing and Genomics Laboratory at University of Helsinki and QB3 at UC Berkeley. Confocal imaging was performed with help from and using equipment of the Light Microscopy Unit (LMU), University of Helsinki. Special thanks to M. Herpola and F. A. Silva for technical help. This work was supported by the Academy of Finland (grant numbers 316544 and 346141 to G.E., X.Z., R.M., B.W., L.V., M.L.G., T.B., O.S., and A.P.M.; 343527 to A.P.; 326036, 347130, 353537, and 346141 to M.K.T.), the European Research Council (ERC-CoG CORKtheCAMBIA agreement 819422 to G.E., X.Z., H.I., J.L.O., R.M., B.W., X.W., J.Z., and A.P.M.), the University of Helsinki (ILS to G.E. and DPPS to R.M. and L.V.), EMBO (Postdoctoral Fellowship ALTF 1235-2020 to X.Z. and ALTF 128-2020 to H.I.), JSPS (Overseas Research Fellowship to H.I.), BBSRC (grant BB/V008129/1 to J.P.E., J.H., and A.P.M.), the European Commission (Marie Sk\u0142odowska-Curie Fellowship 329978 to J.P.E. and S.M.B.), and the Dutch Organization for Scientific Research (Nederlandse Organisatie voor Wetenschappelijk Onderzoek, NWO, grant 864.14.003 to J.P.R. and K.t.T. and OCENW. GROOT.2019.017 to B.P.J.). We thank V. Willemsen, K. Prasad, and B. Krizek for providing published material and J. Traas for providing the unpublished entry clone containing the AIL6/PLT3 promoter; J. Vainonen for help with protein work; and Y. Helariutta for providing feedback on the manuscript. We acknowledge support for RNA-seq from DNA Sequencing and Genomics Laboratory at University of Helsinki and QB3 at UC Berkeley. Confocal imaging was performed with help from and using equipment of the Light Microscopy Unit (LMU), University of Helsinki. Special thanks to M. Herpola and F. A. Silva for technical help. Funding: This work was supported by the Academy of Finland (grant numbers 316544 and 346141 to G.E., X.Z., R.M., B.W., L.V., M.L.G., T.B., O.S., and A.P.M.; 343527 to A.P.; 326036, 347130, 353537, and 346141 to M.K.T.), the European Research Council (ERC-CoG CORKtheCAMBIA agreement 819422 to G.E., X.Z., H.I., J.L.O., R.M., B.W., X.W., J.Z., and A.P.M.), the University of Helsinki (ILS to G.E. and DPPS to R.M. and L.V.), EMBO (Postdoctoral Fellowship ALTF 1235-2020 to X.Z. and ALTF 128-2020 to H.I.), JSPS (Overseas Research Fellowship to H.I.), BBSRC (grant BB/V008129/1 to J.P.E., J.H., and A.P.M.), the European Commission (Marie Sk\u0142odowska-Curie Fellowship 329978 to J.P.E. and S.M.B.), and the Dutch Organization for Scientific Research (Nederlandse Organisatie voor Wetenschappelijk Onderzoek, NWO, grant 864.14.003 to J.P.R. and K.t.T. and OCENW. GROOT.2019.017 to B.P.J.). Author contributions: K.t.T., J.P.E., and A.P.M. conceived of the project; G.E., X.Z., H.I., J.L.O., O.S., S.M.B., M.K.T., J.P.E., and A.P.M. designed the experiments; G.E., X.Z., J.H., H.I., J.L.O., R.M., B.W., J.Z., M.K.T., and J.P.E. performed the experiments; J.P.R. and K.t.T. designed and performed the computational modeling; B.P.J. and K.t.T. performed the mathematical model analysis; L.V. created the circle-unwrapping projections; A.P. performed statistical analysis; X.W. generated genetic material; M.L.G. provided preliminary data; T.B. and D.D. assisted with RNA-seq analysis; and G.E., X.Z., J.P.R., K.t.T., J.P.E., and A.P.M. wrote the paper, with input from all authors. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All lines involved in this study are available upon reasonable request from the corresponding authors. Gene accession numbers are as follows: ANT, AT4G37750; APL, AT1G79430; AtHB8, AT4G32880; CLE41, AT3G24770; MIR165A, AT1G01183; PEAR1, AT2G37590; PLT1, AT3G20840; PLT2, AT1G51190; PLT3, AT5G10510; PLT4, AT5G17430; PLT5, AT5G57390; PLT7, AT5G65510; PXY/TDR, AT5G61480; VND6, AT5G62380; and PEX4/UBC21 AT5G25760. The data of transcriptomes of pxy and 35S:CLE41 are available in the Gene Expression Omnibus (GEO; accession number GSE119872). The data of transcriptome of 35S:XVE>>PLT5-tagRFP are available in GEO (accession number GSE264403). The source codes for the different models described here are available at https://tbb.bio.uu.nl/ khwjtuss/cambium and in Zenodo (31). License information: Copyright \u00A9 2024 the authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original US government works. https://www.science.org/ about/science-licenses-journal-article-reuse. This research was funded in whole or in part by the Academy of Finland (316544, 346141, 343527, 326036, 347130, and 353537), a cOAlition S organization. The author will make the Author Accepted Manuscript (AAM) version available under a CC BY public copyright license.; http://hdl.handle.net/10138/588647; 85209165432; 001352133200014

الاتاحة: http://hdl.handle.net/10138/588647

المؤلفون: Su, Chang, Kokosza, Andrzej, Xie, Xiaonan, Pěnčík, Aleš, Zhang, Youjun, Raumonen, Pasi, Shi, Xueping, Muranen, Sampo, Topcu, Melis Kucukoglu, Immanen, Juha, Hagqvist, Risto, Safronov, Omid, Alonso-Serra, Juan, Eswaran, Gugan, Venegas, Mirko Pavicic, Ljung, Karin, Ward, Sally, Mähönen, Ari Pekka, Himanen, Kristiina, Salojärvi, Jarkko, Fernie, Alisdair R., Novák, Ondřej, Leyser, Ottoline, Pałubicki, Wojtek, Helariutta, Ykä, Nieminen, Kaisa

المساهمون: Tampere University, Computing Sciences

مصطلحات موضوعية: 111 Mathematics

وصف الملف: fulltext

Relation: e2308587120; 48; 120; ORCID: /0000-0001-5471-0970/work/149283479; https://trepo.tuni.fi/handle/10024/153715; URN:NBN:fi:tuni-2023122211182

الاتاحة: https://trepo.tuni.fi/handle/10024/153715
https://doi.org/10.1073/pnas.2308587120

المؤلفون: Chang Su, Kokosza, Andrzej, Xiaonan Xie, Pěnčík, Aleš, Youjun Zhang, Raumonen, Pasi, Xueping Shi, Muranen, Sampo, Topcu, Melis Kucukoglu, Immanen, Juha, Hagqvist, Risto, Safronov, Omid, Alonso-Serra, Juan, Eswaran, Gugan, Venegas, Mirko Pavicic, Ljung, Karin, Ward, Sally, Mähönen, Ari Pekka, Himanen, Kristiina, Salojärvi, Jarkko

المصدر: Proceedings of the National Academy of Sciences of the United States of America; 11/28/2023, Vol. 120 Issue 48, p1-19, 28p

مصطلحات موضوعية: AUXIN, EUROPEAN white birch, CONCENTRATION gradient, TREES, BIRCH

المؤلفون: Yrjo Helariutta, Melis Kucukoglu Topcu

المصدر: Nature Plants. 9:7-8

مصطلحات موضوعية: Plant Science

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::5cb20ec7c5855378bd7045ce8d054740
https://doi.org/10.1038/s41477-022-01316-6

المؤلفون: Salma Chaabouni, Ykä Helariutta, Bo Zheng, Ari Pekka Mähönen, Ove Nilsson, Melis Kucukoglu

المساهمون: Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre (ViPS), Helsinki Institute of Life Science HiLIFE

المصدر: The New Phytologist

مصطلحات موضوعية: 0106 biological sciences, 0301 basic medicine, Physiology, Secondary growth, Plant Science, 01 natural sciences, 03 medical and health sciences, CLAVATA3, RNA interference, Gene Expression Regulation, Plant, Xylem, Gene expression, Vascular cambium, Gene silencing, Cambium, GENE-EXPRESSION, PttCLE47, Full Paper, Chemistry, Forest Science, Research, fungi, Botany, Meristem, Full Papers, 11831 Plant biology, ARABIDOPSIS, Wood, Cell biology, HD-ZIP, secondary growth and development, 030104 developmental biology, Populus, MERISTEM, CLE peptides, SHOOT, 1182 Biochemistry, cell and molecular biology, wood formation, STEM-CELL FATE, Peptides, CLV3, 010606 plant biology & botany

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::35b0d76964fb086f8faa02eb8e550224
http://europepmc.org/articles/PMC7065007

المؤلفون: Ji-Young Lee, Kaisa Nieminen, Pierre Barbier de Reuille, Jing Zhang, Annakaisa Elo, Jiale Xiang, Juan Alonso-Serra, Weibing Yang, Je-Gun Joung, Ykä Helariutta, Laura Ragni, Ari Pekka Mähönen, Gugan Eswaran, Jae-Young Yun, Teddy Damén, Jung-Hun Lee, Sebastian E. Ahnert, Melis Kucukoglu

المصدر: Nature Plants. 5:1033-1042

مصطلحات موضوعية: 0106 biological sciences, 0301 basic medicine, Secondary growth, fungi, food and beverages, Xylem, Plant Science, Biology, Meristem, biology.organism_classification, 01 natural sciences, Cell biology, 03 medical and health sciences, 030104 developmental biology, Arabidopsis, Transcriptional regulation, Vascular cambium, Cambium, Transcription factor, 010606 plant biology & botany

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::3415395509d5dfdd70db1659c0b62b89
https://doi.org/10.1038/s41477-019-0522-9

المؤلفون: Yrjö Helariutta, Rishikesh P. Bhalerao, Urs Fischer, Melis Kucukoglu

المصدر: Annual Review of Plant Biology. 70:293-319

مصطلحات موضوعية: 0106 biological sciences, 0301 basic medicine, Physiology, Secondary growth, Meristem, Plant Science, Phloem, Biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Xylem, Auxin, Vascular cambium, Molecular Biology, chemistry.chemical_classification, Cambium, Stem Cells, fungi, food and beverages, Cell Biology, Cell biology, 030104 developmental biology, chemistry, Auxin polar transport, Cytokinin, Gibberellin, Stem cell, 010606 plant biology & botany

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe746beee57d42ea8eea250a84cecf82
https://doi.org/10.1146/annurev-arplant-050718-100402

المؤلفون: Melis Kucukoglu

المصدر: New Phytologist. 226:5-7

مصطلحات موضوعية: 0106 biological sciences, Cell division, Physiology, Meristem, Cell, Plant Science, 01 natural sciences, 03 medical and health sciences, Xylem, Arabidopsis, Vascular cambium, medicine, Cambium, Transcription factor, 030304 developmental biology, 0303 health sciences, biology, Arabidopsis Proteins, biology.organism_classification, Cell biology, medicine.anatomical_structure, Cell Division, Transcription Factors, 010606 plant biology & botany

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::af31ad7f3bb0f93874708fb7c5502868
https://doi.org/10.1111/nph.16400

المؤلفون: Urs Fischer, Christoffer Johnsson, Vikash Kumar, Torgeir R. Hvidsten, Totte Niittylä, Chanaka Mannapperuma, Ove Nilsson, David Sundell, Manoj Kumar, Edouard Pesquet, Ewa J. Mellerowicz, Björn Sundberg, Melis Kucukoglu, Nathaniel R. Street, Nicolas Delhomme, Hannele Tuominen

المصدر: The Plant Cell. 29:1585-1604

مصطلحات موضوعية: 0301 basic medicine, Modularity (networks), Carbon sink, Cell Biology, Plant Science, Carbon sequestration, Biology, Transcriptome, 03 medical and health sciences, 030104 developmental biology, Botany, High spatial resolution, Transcriptome Profiles, Biological sciences, Woody plant

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::567134d4a983d74b535bb23cc26d3a30
https://doi.org/10.1105/tpc.17.00153

المؤلفون: Lei Liu, Melis Kucukoglu, Robert M. Larkin, Dongdong Tian, Bo Zheng, Zhe Zhang, Xueping Shi

المصدر: BMC Genomics, Vol 21, Iss 1, Pp 1-2 (2020)

مصطلحات موضوعية: chemistry.chemical_classification, lcsh:QH426-470, lcsh:Biotechnology, Computational biology, Biology, Proteomics, Amino acid, lcsh:Genetics, chemistry, lcsh:TP248.13-248.65, Genetics, DNA microarray, Cluster analysis, Gene, Biotechnology

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::11f56ee0bbeb93543d14aebeb564a7ac
https://doaj.org/article/8b8be2f5529f4e53b7fa270c2e8e7e72

المؤلفون: Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi, Bo Zheng

مصطلحات موضوعية: fungi

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::ee8ecfd2c323b45057208488cd1a40ff
https://doi.org/10.21203/rs.2.21530/v1

المؤلفون: Xueping Shi, Robert M. Larkin, Melis Kucukoglu, Zhe Zhang, Lei Liu, Dongdong Tian, Bo Zheng

المصدر: BMC Genomics
BMC Genomics, Vol 21, Iss 1, Pp 1-17 (2020)

مصطلحات موضوعية: 0106 biological sciences, Signal peptide, lcsh:QH426-470, Evolution, Gene prediction, lcsh:Biotechnology, Computational biology, Biology, Protein Sorting Signals, Proteomics, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, lcsh:TP248.13-248.65, Machine learning, Genetics, Gene family, Cluster Analysis, Amino Acid Sequence, Cluster analysis, Gene, Gene clustering, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Methodology Article, fungi, Correction, Plants, Peptide hormone, Amino acid, lcsh:Genetics, ComputingMethodologies_PATTERNRECOGNITION, chemistry, CLE, DNA microarray, Euclidean distance, Peptides, 010606 plant biology & botany, Biotechnology

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::424920da8596e8e8d8a069dab94ca57f
https://pubmed.ncbi.nlm.nih.gov/33339504

المؤلفون: Jing, Zhang, Gugan, Eswaran, Juan, Alonso-Serra, Melis, Kucukoglu, Jiale, Xiang, Weibing, Yang, Annakaisa, Elo, Kaisa, Nieminen, Teddy, Damén, Je-Gun, Joung, Jae-Young, Yun, Jung-Hun, Lee, Laura, Ragni, Pierre, Barbier de Reuille, Sebastian E, Ahnert, Ji-Young, Lee, Ari Pekka, Mähönen, Ykä, Helariutta

المصدر: Nature plants. 5(10)

مصطلحات موضوعية: Cambium, Genotype, Transcription, Genetic, Gene Expression Regulation, Plant, Arabidopsis, Plant Development, Transcriptome, Plant Roots, Transcription Factors

URL الوصول: https://explore.openaire.eu/search/publication?articleId=pmid________::625be38da84bb8c9abef0474caae9851
https://pubmed.ncbi.nlm.nih.gov/31595064

المؤلفون: Ove Nilsson, Melis Kucukoglu

المصدر: Physiologia Plantarum. 155:74-87

مصطلحات موضوعية: Physiology, Meristem, Arabidopsis, Plant Science, Protein Sorting Signals, Biology, Endosperm, Gene Expression Regulation, Plant, Genetics, Gene family, Phylogeny, Regulation of gene expression, Arabidopsis Proteins, Gene Expression Profiling, Stem Cells, fungi, Gene Expression Regulation, Developmental, food and beverages, Embryo, Cell Biology, General Medicine, biology.organism_classification, Cell biology, Signal transduction, Stem cell, Signal Transduction

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e377c20336e366fe62a23ea280ba23b3
https://doi.org/10.1111/ppl.12358

المؤلفون: Fatz, Wiktoria, Woodward, George Malcolm, Vainio, Leo, Topcu, Melis Kucukoglu

المصدر: Encyclopedia of Life Sciences ; page 1-10 ; ISBN 9780470016176 9780470015902

الاتاحة: http://dx.doi.org/10.1002/9780470015902.a0029558
https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470015902.a0029558

المؤلفون: Ove Nilsson, Melis Kucukoglu, Jeanette Nilsson, Salma Chaabouni, Bo Zheng

المصدر: The New phytologist. 215(2)

مصطلحات موضوعية: 0301 basic medicine, Cell division, Physiology, Secondary growth, Plant Science, 03 medical and health sciences, Auxin, Gene Expression Regulation, Plant, Plant Cells, Botany, Vascular cambium, Arabidopsis thaliana, Cambium, Phylogeny, Plant Proteins, chemistry.chemical_classification, biology, Indoleacetic Acids, Plant Stems, fungi, Meristem, biology.organism_classification, Plants, Genetically Modified, 030104 developmental biology, Populus, chemistry, Dormancy, Cell Division

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::07ff53135a46b5278c903d9a0572a86b
https://pubmed.ncbi.nlm.nih.gov/28609015

المؤلفون: David, Sundell, Nathaniel R, Street, Manoj, Kumar, Ewa J, Mellerowicz, Melis, Kucukoglu, Christoffer, Johnsson, Vikash, Kumar, Chanaka, Mannapperuma, Nicolas, Delhomme, Ove, Nilsson, Hannele, Tuominen, Edouard, Pesquet, Urs, Fischer, Totte, Niittylä, Björn, Sundberg, Torgeir R, Hvidsten

المصدر: The Plant cell. 29(7)

مصطلحات موضوعية: Internet, Populus, Cell Wall, Gene Expression Regulation, Plant, Polysaccharides, Xylem, Meristem, Large-Scale Biology Article, Transcriptome, Wood

URL الوصول: https://explore.openaire.eu/search/publication?articleId=pmid________::5eec368131c3df4b8bb406d9bfdfd1c6
https://pubmed.ncbi.nlm.nih.gov/28655750

المؤلفون: Urs Fischer, Hannele Tuominen, Chanaka Mannapperuma, Torgeir R. Hvidsten, Melis Kucukoglu, Christoffer Johnsson, Ewa J. Mellerowicz, Totte Niittylä, Ove Nilsson, David Sundell, Nathaniel R. Street, Manoj Kumar, Nicolas Delhomme, Björn Sundberg, Edouard Pesquet, Vikash Kumar

مصطلحات موضوعية: Transcriptome, Intergenic region, Vascular cambium, Xylem, RNA, Computational biology, Phloem, Biology, Secondary cell wall, Gene

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1938d460fc825c6a7e19bb62b38e78dc