Reference ID	Paper title	Authors	Journal	Publication year	DOI	Paper URL	Relationship to resource	Verification URL	Verification date
REF001	Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum	Tao Lin; Xia Xu; Huilong Du; Xiuli Fan; Qingwen Chen; Chunyan Hai; Zijian Zhou; Xiao Su; Liquan Kou; Qiang Gao; Lingwei Deng; Jinsheng Jiang; Hanli You; Yihua Ma; Zhukuan Cheng; Guodong Wang; Chengzhi Liang; Guomin Zhang; Hong Yu; Jiayang Li	Science China Life Sciences	2022	10.1007/s11427-021-2033-2	https://doi.org/10.1007/s11427-021-2033-2	Original reference genome publication	https://ngdc.cncb.ac.cn/gwh/api/public/assembly/GWHBCHF00000000; https://api.crossref.org/works/10.1007/s11427-021-2033-2; https://link.springer.com/article/10.1007/s11427-021-2033-2	2026-10-03
REF002	Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis	Tao Lin; Xia Xu; Jue Ruan; Shizhong Liu; Shigang Wu; Xiujuan Shao; Xiaobo Wang; Lin Gan; Bi Qin; Yushuang Yang; Zhukuan Cheng; Suhua Yang; Zhonghua Zhang; Guosheng Xiong; Sanwen Huang; Hong Yu; Jiayang Li	National Science Review	2018	10.1093/nsr/nwx101	https://doi.org/10.1093/nsr/nwx101	Original reference genome publication	https://ngdc.cncb.ac.cn/gwh/api/public/assembly/GWHAAAA00000000; https://api.crossref.org/works/10.1093/nsr/nwx101; https://academic.oup.com/nsr/article/5/1/78/4093910	2026-10-03
REF003	Geranyl Diphosphate Synthases GDS 1 and GDS7 Facilitate Natural Rubber Biosynthesis in Taraxacum kok-saghyz Roots	Baoqiang Wang; Boxuan Yuan; Guoen Ao; Xiaoyou Wu; Fengyan Fang; Shiqi Long; Shugang Hui	Plants	2025	10.3390/plants14192980	https://www.mdpi.com/2223-7747/14/19/2980	verified_article_reuse_accession_origin_not_established	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1262623; https://api.crossref.org/works/10.3390/plants14192980; https://www.mdpi.com/2223-7747/14/19/2980	2026-10-03
REF004	Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs	Zinan Luo; Brian J. Iaffaldano; Xiaofeng Zhuang; Jonathan Fresnedo-Ramírez; Katrina Cornish	Scientific Reports	2017	10.1038/s41598-017-09034-2	https://pmc.ncbi.nlm.nih.gov/articles/PMC5577190/	verified_article_run_accession_to_bioproject	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA361575; https://pmc.ncbi.nlm.nih.gov/articles/PMC5577190/; https://www.ncbi.nlm.nih.gov/sra/SRR5181661; https://api.crossref.org/works/10.1038/s41598-017-09034-2	2026-10-03
REF005	Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants	Francesco Panara; Loredana Lopez; Loretta Daddiego; Elio Fantini; Paolo Facella; Gaetano Perrotta	BMC Genomics	2018	10.1186/s12864-018-5287-4	https://pmc.ncbi.nlm.nih.gov/articles/PMC6280347/	verified_bioproject_publication_and_article_accession; Original data or author-supplied supplementary material publication	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA413689; https://api.crossref.org/works/10.1186/s12864-018-5287-4; https://pmc.ncbi.nlm.nih.gov/articles/PMC6280347/	2026-10-03
REF006	Genome-Wide Identification and Characterization of the HMGR Gene Family in Taraxacum kok-saghyz Provide Insights into Its Regulation in Response to Ethylene and Methyl Jsamonate Treatments	Pingping Du; Huan He; Jiayin Wang; Lili Wang; Zhuang Meng; Xiang Jin; Liyu Zhang; Fei Wang; Hongbin Li; Quanliang Xie	Plants	2024	10.3390/plants13182646	https://pmc.ncbi.nlm.nih.gov/articles/PMC11435204/	verified_article_reuse_accession_origin_not_established	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA539838; https://pmc.ncbi.nlm.nih.gov/articles/PMC11435204/; https://www.mdpi.com/2223-7747/13/18/2646; https://api.crossref.org/works/10.1016/j.indcrop.2022.114776	2026-10-03
REF007	"The
                    Chrysanthemum lavandulifolium
                    genome and the molecular mechanism underlying diverse capitulum types"	Xiaohui Wen; Junzhuo Li; Lili Wang; Chenfei Lu; Qiang Gao; Peng Xu; Ya Pu; Qiuling Zhang; Yan Hong; Luo Hong; He Huang; Huaigen Xin; Xiaoyun Wu; Dongru Kang; Kang Gao; Yajun Li; Chaofeng Ma; Xuming Li; Hongkun Zheng; Zicheng Wang; Yuannian Jiao; Liangsheng Zhang; Silan Dai	Horticulture Research	2022	10.1093/hr/uhab022	https://academic.oup.com/hr/article/doi/10.1093/hr/uhab022/6510191	verified_bioproject_publication_and_article_accession	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA681093; https://api.crossref.org/works/10.1093/hr/uhab022; https://academic.oup.com/hr/article/doi/10.1093/hr/uhab022/6510191; https://www.ncbi.nlm.nih.gov/sra/SRR15099898	2026-10-03
REF008	Transcriptome analysis of Taraxacum kok-saghyz reveals the role of exogenous methyl jasmonate in regulating rubber biosynthesis and drought tolerance	Gaoquan Dong; Hainan Wang; Jiyan Qi; Yadong Leng; Jun Huang; Hao Zhang; Jie Yan	Gene	2023	10.1016/j.gene.2023.147346	https://pubmed.ncbi.nlm.nih.gov/36898514/	candidate_article_metadata_verified_accession_link_not_verified	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA745038; https://api.crossref.org/works/10.1016/j.gene.2023.147346; https://pubmed.ncbi.nlm.nih.gov/36898514/	2026-10-03
REF009	Metabolic and Transcriptomic Analyses Reveal the Effects of Ethephon on Taraxacum kok-saghyz Rodin	Zhanjiang Zhang; Guang Shen; Yihua Yang; Cui Li; Xiaoying Chen; Xiaonan Yang; Xiaoyun Guo; Jianhua Miao; Li Li; Ming Lei	Molecules	2022	10.3390/molecules27113548	https://pmc.ncbi.nlm.nih.gov/articles/PMC9182187/	verified_article_accession	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA827459; https://api.crossref.org/works/10.3390/molecules27113548; https://pmc.ncbi.nlm.nih.gov/articles/PMC9182187/	2026-10-03
REF010	Enhanced natural rubber production in rubber dandelion Taraxacum kok-saghyz roots by foliar application of a natural lipid	Jong-Chan Park; Tengfang Ling; Mi Young Kim; Sung Woo Bae; Stephen Beungtae Ryu	Industrial Crops and Products	2024	10.1016/j.indcrop.2023.117714	https://www.sciencedirect.com/science/article/pii/S0926669023014796	candidate_article_metadata_verified_accession_link_not_verified	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA918839; https://api.crossref.org/works/10.1016/j.indcrop.2023.117714; https://www.sciencedirect.com/science/article/pii/S0926669023014796	2026-10-03
REF011	Overexpression of a pseudo-etiolated-in-light-like protein in Taraxacum koksaghyz leads to a pale green phenotype and enables transcriptome-based network analysis of photomorphogenesis and isoprenoid biosynthesis	Silva Melissa Wolters; Vincent Alexander Benninghaus; Kai-Uwe Roelfs; Nicole van Deenen; Richard M. Twyman; Dirk Prüfer; Christian Schulze Gronover	Frontiers in Plant Science	2023	10.3389/fpls.2023.1228961	https://pmc.ncbi.nlm.nih.gov/articles/PMC10569127/	verified_article_accession	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA985648; https://api.crossref.org/works/10.3389/fpls.2023.1228961; https://pmc.ncbi.nlm.nih.gov/articles/PMC10569127/	2026-10-03
REF012	Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology	Vincent Alexander Benninghaus; Nicole van Deenen; Boje Müller; Kai-Uwe Roelfs; Ines Lassowskat; Iris Finkemeier; Dirk Prüfer; Christian Schulze Gronover	Journal of Experimental Botany	2020	10.1093/jxb/erz512	https://doi.org/10.1093/jxb/erz512	Original data or author-supplied supplementary material publication	https://www.ebi.ac.uk/pride/ws/archive/v2/projects/PXD011773; https://proteomecentral.proteomexchange.org/dataset/PXD011773; https://api.crossref.org/works/10.1093/jxb/erz512; https://pmc.ncbi.nlm.nih.gov/articles/PMC7031084/	2026-10-03
REF013	Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin	Yushuang Yang; Bi Qin; Qiuhui Chen; Qiuhai Nie; Jichuan Zhang; Liqun Zhang; Shizhong Liu	BMC Genomics	2023	10.1186/s12864-022-09105-3	https://doi.org/10.1186/s12864-022-09105-3	Original data or author-supplied supplementary material publication; Original resequencing publication	https://link.springer.com/article/10.1186/s12864-022-09105-3; https://api.crossref.org/works/10.1186/s12864-022-09105-3; https://ngdc.cncb.ac.cn/gsa/browse/CRA009020	2026-10-03
REF014	LocPro: A deep learning-based prediction of protein subcellular localization for promoting multi-directional pharmaceutical research	Yintao Zhang; Lingyan Zheng; Nanxin You; Wei Hu; Wanghao Jiang; Mingkun Lu; Hangwei Xu; Haibin Dai; Tingting Fu; Ying Zhou	Journal of Pharmaceutical Analysis	2025	10.1016/j.jpha.2025.101255	https://doi.org/10.1016/j.jpha.2025.101255	Software methods publication	https://jpa.xjtu.edu.cn/article/doi/10.1016/j.jpha.2025.101255?pageType=en; https://api.crossref.org/works/10.1016%2Fj.jpha.2025.101255; https://github.com/idrblab/LocPro	2026-10-03
REF015	Evolutionary-scale prediction of atomic-level protein structure with a language model	Zeming Lin; Halil Akin; Roshan Rao; Brian Hie; Zhongkai Zhu; Wenting Lu; Nikita Smetanin; Robert Verkuil; Ori Kabeli; Yaniv Shmueli; Allan dos Santos Costa; Maryam Fazel-Zarandi; Tom Sercu; Salvatore Candido; Alexander Rives	Science	2023	10.1126/science.ade2574	https://doi.org/10.1126/science.ade2574	Software methods publication	https://github.com/facebookresearch/esm; https://api.crossref.org/works/10.1126%2Fscience.ade2574	2026-10-03
REF016	Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence	H. B. Rao; F. Zhu; G. B. Yang; Z. R. Li; Y. Z. Chen	Nucleic Acids Research	2011	10.1093/nar/gkr284	https://doi.org/10.1093/nar/gkr284	Software methods publication	https://pmc.ncbi.nlm.nih.gov/articles/PMC3125735/; https://api.crossref.org/works/10.1093%2Fnar%2Fgkr284	2026-10-03
REF017	Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype	Daehwan Kim; Joseph M. Paggi; Chanhee Park; Christopher Bennett; Steven L. Salzberg	Nature Biotechnology	2019	10.1038/s41587-019-0201-4	https://doi.org/10.1038/s41587-019-0201-4	Software methods publication	https://www.nature.com/articles/s41587-019-0201-4; https://api.crossref.org/works/10.1038%2Fs41587-019-0201-4	2026-10-03
REF018	StringTie enables improved reconstruction of a transcriptome from RNA-seq reads	Mihaela Pertea; Geo M Pertea; Corina M Antonescu; Tsung-Cheng Chang; Joshua T Mendell; Steven L Salzberg	Nature Biotechnology	2015	10.1038/nbt.3122	https://doi.org/10.1038/nbt.3122	Software methods publication	https://www.nature.com/articles/nbt.3122; https://api.crossref.org/works/10.1038%2Fnbt.3122	2026-10-03
REF019	Twelve years of SAMtools and BCFtools	Petr Danecek; James K Bonfield; Jennifer Liddle; John Marshall; Valeriu Ohan; Martin O Pollard; Andrew Whitwham; Thomas Keane; Shane A McCarthy; Robert M Davies; Heng Li	GigaScience	2021	10.1093/gigascience/giab008	https://doi.org/10.1093/gigascience/giab008	Software methods publication	https://pmc.ncbi.nlm.nih.gov/articles/PMC7931819/; https://api.crossref.org/works/10.1093%2Fgigascience%2Fgiab008	2026-10-03
REF020	BLAST+: architecture and applications	Christiam Camacho; George Coulouris; Vahram Avagyan; Ning Ma; Jason Papadopoulos; Kevin Bealer; Thomas L Madden	BMC Bioinformatics	2009	10.1186/1471-2105-10-421	https://doi.org/10.1186/1471-2105-10-421	Software methods publication	https://doi.org/10.1186/1471-2105-10-421; https://api.crossref.org/works/10.1186%2F1471-2105-10-421	2026-10-03
REF021	Accelerated Profile HMM Searches	Sean R. Eddy	PLoS Computational Biology	2011	10.1371/journal.pcbi.1002195	https://doi.org/10.1371/journal.pcbi.1002195	Software methods publication	https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002195; https://api.crossref.org/works/10.1371%2Fjournal.pcbi.1002195	2026-10-03
REF022	FIMO: scanning for occurrences of a given motif	Charles E. Grant; Timothy L. Bailey; William Stafford Noble	Bioinformatics	2011	10.1093/bioinformatics/btr064	https://doi.org/10.1093/bioinformatics/btr064	Software methods publication	https://meme-suite.org/meme/doc/fimo.html?man_type=web; https://api.crossref.org/works/10.1093%2Fbioinformatics%2Fbtr064	2026-10-03
REF023	Sensitive protein alignments at tree-of-life scale using DIAMOND	Benjamin Buchfink; Klaus Reuter; Hajk-Georg Drost	Nature Methods	2021	10.1038/s41592-021-01101-x	https://doi.org/10.1038/s41592-021-01101-x	Software methods publication	https://github.com/bbuchfink/diamond/blob/master/README.md; https://api.crossref.org/works/10.1038%2Fs41592-021-01101-x	2026-10-03
REF024	JCVI: A versatile toolkit for comparative genomics analysis	Haibao Tang; Vivek Krishnakumar; Xiaofei Zeng; Zhougeng Xu; Adam Taranto; Johnathan S. Lomas; Yixing Zhang; Yumin Huang; Yibin Wang; Won Cheol Yim; Jisen Zhang; Xingtan Zhang	iMeta	2024	10.1002/imt2.211	https://doi.org/10.1002/imt2.211	Software methods publication	https://pmc.ncbi.nlm.nih.gov/articles/PMC11316928/; https://api.crossref.org/works/10.1002%2Fimt2.211	2026-10-03
REF025	Minimap2: pairwise alignment for nucleotide sequences	Heng Li	Bioinformatics	2018	10.1093/bioinformatics/bty191	https://doi.org/10.1093/bioinformatics/bty191	Software methods publication	https://github.com/lh3/minimap2; https://github.com/lh3/minimap2/releases; https://api.crossref.org/works/10.1093%2Fbioinformatics%2Fbty191	2026-10-03
REF026	KMC 3: counting and manipulating k-mer statistics	Marek Kokot; Maciej Długosz; Sebastian Deorowicz	Bioinformatics	2017	10.1093/bioinformatics/btx304	https://doi.org/10.1093/bioinformatics/btx304	Software methods publication	https://github.com/refresh-bio/KMC; https://github.com/refresh-bio/KMC/releases; https://api.crossref.org/works/10.1093%2Fbioinformatics%2Fbtx304	2026-10-03
REF027	MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification	Jürgen Cox; Matthias Mann	Nature Biotechnology	2008	10.1038/nbt.1511	https://doi.org/10.1038/nbt.1511	Software methods publication	https://www.maxquant.org/maxquant/; https://api.crossref.org/works/10.1038%2Fnbt.1511	2026-10-03
REF028	featureCounts: an efficient general purpose program for assigning sequence reads to genomic features	Yang Liao; Gordon K. Smyth; Wei Shi	Bioinformatics	2014	10.1093/bioinformatics/btt656	https://doi.org/10.1093/bioinformatics/btt656	Software methods publication	https://subread.sourceforge.net/; https://api.crossref.org/works/10.1093%2Fbioinformatics%2Fbtt656	2026-10-03
REF029	JBrowse 2: a modular genome browser with views of synteny and structural variation	Colin Diesh; Garrett J Stevens; Peter Xie; Teresa De Jesus Martinez; Elliot A. Hershberg; Angel Leung; Emma Guo; Shihab Dider; Junjun Zhang; Caroline Bridge; Gregory Hogue; Andrew Duncan; Matthew Morgan; Tia Flores; Benjamin N. Bimber; Robin Haw; Scott Cain; Robert M. Buels; Lincoln D. Stein; Ian H. Holmes	Genome Biology	2023	10.1186/s13059-023-02914-z	https://doi.org/10.1186/s13059-023-02914-z	Software methods publication	https://jbrowse.org/jb2-staging/docs/faq/; https://api.crossref.org/works/10.1186%2Fs13059-023-02914-z	2026-10-03
REF030	Array programming with NumPy	Charles R. Harris; K. Jarrod Millman; Stéfan J. van der Walt; Ralf Gommers; Pauli Virtanen; David Cournapeau; Eric Wieser; Julian Taylor; Sebastian Berg; Nathaniel J. Smith; Robert Kern; Matti Picus; Stephan Hoyer; Marten H. van Kerkwijk; Matthew Brett; Allan Haldane; Jaime Fernández del Río; Mark Wiebe; Pearu Peterson; Pierre Gérard-Marchant; Kevin Sheppard; Tyler Reddy; Warren Weckesser; Hameer Abbasi; Christoph Gohlke; Travis E. Oliphant	Nature	2020	10.1038/s41586-020-2649-2	https://doi.org/10.1038/s41586-020-2649-2	Software methods publication	https://api.crossref.org/works/10.1038/s41586-020-2649-2	2026-10-03
REF031	Data Structures for Statistical Computing in Python	Wes McKinney	Proceedings of the Python in Science Conference	2010	10.25080/majora-92bf1922-00a	https://doi.org/10.25080/Majora-92bf1922-00a	Software methods publication	https://api.crossref.org/works/10.25080/Majora-92bf1922-00a	2026-10-03
REF032	PyTorch: An Imperative Style, High-Performance Deep Learning Library	Paszke, Adam; Gross, Sam; Massa, Francisco; Lerer, Adam; Bradbury, James; Chanan, Gregory; Killeen, Trevor; Lin, Zeming; Gimelshein, Natalia; Antiga, Luca; Desmaison, Alban; Kopf, Andreas; Yang, Edward; DeVito, Zachary; Raison, Martin; Tejani, Alykhan; Chilamkurthy, Sasank; Steiner, Benoit; Fang, Lu; Bai, Junjie; Chintala, Soumith	Advances in Neural Information Processing Systems 32	2019		https://proceedings.neurips.cc/paper/2019/hash/bdbca288fee7f92f2bfa9f7012727740-Abstract.html	Official technical documentation; no specific methods paper	https://proceedings.neurips.cc/paper/2019/hash/bdbca288fee7f92f2bfa9f7012727740-Abstract.html	2026-10-03
REF033	UniProt: the Universal Protein Knowledgebase in 2025	The UniProt Consortium; Alex Bateman; Maria-Jesus Martin; Sandra Orchard; Michele Magrane; Aduragbemi Adesina; Shadab Ahmad; Emily H Bowler-Barnett; Hema Bye-A-Jee; David Carpentier; Paul Denny; Jun Fan; Penelope Garmiri; Leonardo Jose da Costa Gonzales; Abdulrahman Hussein; Alexandr Ignatchenko; Giuseppe Insana; Rizwan Ishtiaq; Vishal Joshi; Dushyanth Jyothi; Swaathi Kandasaamy; Antonia Lock; Aurelien Luciani; Jie Luo; Yvonne Lussi; Juan Sebastian Martinez Marin; Pedro Raposo; Daniel L Rice; Rafael Santos; Elena Speretta; James Stephenson; Prabhat Totoo; Nidhi Tyagi; Nadya Urakova; Preethi Vasudev; Kate Warner; Supun Wijerathne; Conny Wing-Heng Yu; Rossana Zaru; Alan J Bridge; Lucila Aimo; Ghislaine Argoud-Puy; Andrea H Auchincloss; Kristian B Axelsen; Parit Bansal; Delphine Baratin; Teresa M Batista Neto; Marie-Claude Blatter; Jerven T Bolleman; Emmanuel Boutet; Lionel Breuza; Blanca Cabrera Gil; Cristina Casals-Casas; Kamal Chikh Echioukh; Elisabeth Coudert; Beatrice Cuche; Edouard de Castro; Anne Estreicher; Maria L Famiglietti; Marc Feuermann; Elisabeth Gasteiger; Pascale Gaudet; Sebastien Gehant; Vivienne Gerritsen; Arnaud Gos; Nadine Gruaz; Chantal Hulo; Nevila Hyka-Nouspikel; Florence Jungo; Arnaud Kerhornou; Philippe Le Mercier; Damien Lieberherr; Patrick Masson; Anne Morgat; Salvo Paesano; Ivo Pedruzzi; Sandrine Pilbout; Lucille Pourcel; Sylvain Poux; Monica Pozzato; Manuela Pruess; Nicole Redaschi; Catherine Rivoire; Christian J A Sigrist; Karin Sonesson; Shyamala Sundaram; Anastasia Sveshnikova; Cathy H Wu; Cecilia N Arighi; Chuming Chen; Yongxing Chen; Hongzhan Huang; Kati Laiho; Minna Lehvaslaiho; Peter McGarvey; Darren A Natale; Karen Ross; C R Vinayaka; Yuqi Wang; Jian Zhang	Nucleic Acids Research	2025	10.1093/nar/gkae1010	https://doi.org/10.1093/nar/gkae1010	Database resource publication	https://www.uniprot.org/help/publications; https://api.crossref.org/works/10.1093%2Fnar%2Fgkae1010	2026-10-03
REF034	Pfam: The protein families database in 2021	Jaina Mistry; Sara Chuguransky; Lowri Williams; Matloob Qureshi; Gustavo A Salazar; Erik L L Sonnhammer; Silvio C E Tosatto; Lisanna Paladin; Shriya Raj; Lorna J Richardson; Robert D Finn; Alex Bateman	Nucleic Acids Research	2021	10.1093/nar/gkaa913	https://doi.org/10.1093/nar/gkaa913	Database resource publication	https://doi.org/10.1093/nar/gkaa913; https://api.crossref.org/works/10.1093%2Fnar%2Fgkaa913	2026-10-03
REF035	The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest	Damian Szklarczyk; Rebecca Kirsch; Mikaela Koutrouli; Katerina Nastou; Farrokh Mehryary; Radja Hachilif; Annika L Gable; Tao Fang; Nadezhda T Doncheva; Sampo Pyysalo; Peer Bork; Lars J Jensen; Christian von Mering	Nucleic Acids Research	2023	10.1093/nar/gkac1000	https://doi.org/10.1093/nar/gkac1000	Database resource publication	https://string-db.org/cgi/about; https://api.crossref.org/works/10.1093%2Fnar%2Fgkac1000	2026-10-03
REF036	JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles	Ieva Rauluseviciute; Rafael Riudavets-Puig; Romain Blanc-Mathieu; Jaime A Castro-Mondragon; Katalin Ferenc; Vipin Kumar; Roza Berhanu Lemma; Jérémy Lucas; Jeanne Chèneby; Damir Baranasic; Aziz Khan; Oriol Fornes; Sveinung Gundersen; Morten Johansen; Eivind Hovig; Boris Lenhard; Albin Sandelin; Wyeth W Wasserman; François Parcy; Anthony Mathelier	Nucleic Acids Research	2024	10.1093/nar/gkad1059	https://doi.org/10.1093/nar/gkad1059	Database resource publication	https://jaspar.elixir.no/faq/; https://api.crossref.org/works/10.1093%2Fnar%2Fgkad1059	2026-10-03
REF037	PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants	Jinpu Jin; Feng Tian; De-Chang Yang; Yu-Qi Meng; Lei Kong; Jingchu Luo; Ge Gao	Nucleic Acids Research	2017	10.1093/nar/gkw982	https://doi.org/10.1093/nar/gkw982	Database resource publication	https://planttfdb.gao-lab.org/; https://api.crossref.org/works/10.1093%2Fnar%2Fgkw982	2026-10-03
REF038	3did: a catalog of domain-based interactions of known three-dimensional structure	Roberto Mosca; Arnaud Céol; Amelie Stein; Roger Olivella; Patrick Aloy	Nucleic Acids Research	2014	10.1093/nar/gkt887	https://doi.org/10.1093/nar/gkt887	Database resource publication	https://3did.irbbarcelona.org/; https://api.crossref.org/works/10.1093%2Fnar%2Fgkt887	2026-10-03
REF039	Gene Ontology: tool for the unification of biology	Michael Ashburner; Catherine A. Ball; Judith A. Blake; David Botstein; Heather Butler; J. Michael Cherry; Allan P. Davis; Kara Dolinski; Selina S. Dwight; Janan T. Eppig; Midori A. Harris; David P. Hill; Laurie Issel-Tarver; Andrew Kasarskis; Suzanna Lewis; John C. Matese; Joel E. Richardson; Martin Ringwald; Gerald M. Rubin; Gavin Sherlock	Nature Genetics	2000	10.1038/75556	https://doi.org/10.1038/75556	Database resource publication	https://geneontology.org/docs/go-citation-policy/; https://geneontology.org/docs/download-ontology/; https://api.crossref.org/works/10.1038%2F75556	2026-10-03
REF040	KEGG: biological systems database as a model of the real world	Minoru Kanehisa; Miho Furumichi; Yoko Sato; Yuriko Matsuura; Mari Ishiguro-Watanabe	Nucleic Acids Research	2025	10.1093/nar/gkae909	https://doi.org/10.1093/nar/gkae909	Database resource publication	https://www.kegg.jp/; https://www.kegg.jp/kegg/rest/; https://api.crossref.org/works/10.1093%2Fnar%2Fgkae909; https://pubmed.ncbi.nlm.nih.gov/39417505/	2026-10-03
REF041	Identification and reconstitution of the rubber biosynthetic machinery on rubber particles from Hevea brasiliensis	Satoshi Yamashita; Haruhiko Yamaguchi; Toshiyuki Waki; Yuichi Aoki; Makie Mizuno; Fumihiro Yanbe; Tomoki Ishii; Ayuta Funaki; Yuzuru Tozawa; Yukino Miyagi-Inoue; Kazuhisa Fushihara; Toru Nakayama; Seiji Takahashi	eLife	2016	10.7554/elife.19022	https://doi.org/10.7554/eLife.19022	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.7554/eLife.19022	2026-10-03
REF042	"Molecular cloning, expression and characterization of cDNA encoding
                    cis
                    ‐prenyltransferases from
                    Hevea brasiliensis"	Kasem Asawatreratanakul; Yuan‐Wei Zhang; Dhirayos Wititsuwannakul; Rapepun Wititsuwannakul; Seiji Takahashi; Atiya Rattanapittayaporn; Tanetoshi Koyama	European Journal of Biochemistry	2003	10.1046/j.1432-1033.2003.03863.x	https://doi.org/10.1046/j.1432-1033.2003.03863.x	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1046/j.1432-1033.2003.03863.x	2026-10-03
REF043	Molecular Studies of the Protein Complexes Involving Cis-Prenyltransferase in Guayule (Parthenium argentatum), an Alternative Rubber-Producing Plant	Adam M. Lakusta; Moonhyuk Kwon; Eun-Joo G. Kwon; Solomon Stonebloom; Henrik V. Scheller; Dae-Kyun Ro	Frontiers in Plant Science	2019	10.3389/fpls.2019.00165	https://doi.org/10.3389/fpls.2019.00165	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.3389/fpls.2019.00165	2026-10-03
REF044	Reconstitution of prenyltransferase activity on nanodiscs by components of the rubber synthesis machinery of the Para rubber tree and guayule	Fu Kuroiwa; Akira Nishino; Yasuko Mandal; Masataka Honzawa; Miki Suenaga-Hiromori; Kakeru Suzuki; Yukie Takani; Yukino Miyagi-Inoue; Haruhiko Yamaguchi; Satoshi Yamashita; Seiji Takahashi; Yuzuru Tozawa	Scientific Reports	2022	10.1038/s41598-022-07564-y	https://doi.org/10.1038/s41598-022-07564-y	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1038/s41598-022-07564-y	2026-10-03
REF045	Downregulation of a CYP74 Rubber Particle Protein Increases Natural Rubber Production in Parthenium argentatum	Dante F. Placido; Niu Dong; Chen Dong; Von Mark V. Cruz; David A. Dierig; Rebecca E. Cahoon; Byung-guk Kang; Trinh Huynh; Maureen Whalen; Grisel Ponciano; Colleen McMahan	Frontiers in Plant Science	2019	10.3389/fpls.2019.00760	https://doi.org/10.3389/fpls.2019.00760	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.3389/fpls.2019.00760	2026-10-03
REF046	RNASeq analysis of drought-stressed guayule reveals the role of gene transcription for modulating rubber, resin, and carbohydrate synthesis	Chen Dong; Grisel Ponciano; Naxin Huo; Yong Gu; Daniel Ilut; Colleen McMahan	Scientific Reports	2021	10.1038/s41598-021-01026-7	https://doi.org/10.1038/s41598-021-01026-7	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1038/s41598-021-01026-7	2026-10-03
REF047	Transcriptome analysis of rubber biosynthesis in guayule (Parthenium argentatum gray)	Solomon H. Stonebloom; Henrik Vibe Scheller	BMC Plant Biology	2019	10.1186/s12870-019-1669-2	https://doi.org/10.1186/s12870-019-1669-2	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1186/s12870-019-1669-2	2026-10-03
REF048	Characterization of Small Rubber Particle Protein 1 promoter from guayule (Parthenium argentatum)	Grisel Ponciano; Niu Dong; Chen Dong; Kumiko Johnson; Tina Williams; Delilah F. Wood; Grace Chen	BMC Research Notes	2025	10.1186/s13104-025-07448-0	https://doi.org/10.1186/s13104-025-07448-0	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1186/s13104-025-07448-0	2026-10-03
REF049	Laticifer-Specific cis-Prenyltransferase Silencing Affects the Rubber, Triterpene, and Inulin Content of Taraxacum brevicorniculatum	Janina Post; Nicole van Deenen; Julia Fricke; Natalie Kowalski; David Wurbs; Hubert Schaller; Wolfgang Eisenreich; Claudia Huber; Richard M. Twyman; Dirk Prüfer; Christian Schulze Gronover	Plant Physiology	2012	10.1104/pp.111.187880	https://doi.org/10.1104/pp.111.187880	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1104/pp.111.187880	2026-10-03
REF050	Small rubber particle proteins from Taraxacum brevicorniculatum promote stress tolerance and influence the size and distribution of lipid droplets and artificial poly(cis‐1,4‐isoprene) bodies	Natalie Laibach; Sina Schmidl; Boje Müller; Maike Bergmann; Dirk Prüfer; Christian Schulze Gronover	The Plant Journal	2018	10.1111/tpj.13829	https://doi.org/10.1111/tpj.13829	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1111/tpj.13829	2026-10-03
REF051	Structure and biosynthesis of trans-polyisoprene from Eucommia ulmoides	Jitladda Tangpakdee; Yasuyuki Tanaka; Ken-ichi Shiba; Seiichi Kawahara; Koji Sakurai; Yoshihisa Suzuki	Phytochemistry	1997	10.1016/s0031-9422(96)00806-0	https://doi.org/10.1016/S0031-9422(96)00806-0	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1016/S0031-9422(96)00806-0	2026-10-03
REF052	Overexpression of an isopentenyl diphosphate isomerase gene to enhance trans-polyisoprene production in Eucommia ulmoides Oliver	Ren Chen; Yoko Harada; Takeshi Bamba; Yoshihisa Nakazawa; Koichiro Gyokusen	BMC Biotechnology	2012	10.1186/1472-6750-12-78	https://doi.org/10.1186/1472-6750-12-78	Evidence in the original species; not experimental validation in Taraxacum kok-saghyz	https://api.crossref.org/works/10.1186/1472-6750-12-78	2026-10-03