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  1. Scholars Hub of the Academia Sinica
Academia Sinica / Division of Life Sciences / Agricultural Biotechnology Research Center

Lin, Yao-Cheng

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Issue DateTitleAuthor(s)RelationscopusWOSFulltext/Archive link
12023Complete Genome Sequence Resource of Pectobacterium colocasium Strain F1-1 that Causes Soft Rot Disease of TaroHuang, Chien-Jui; Wu, Ting-Li; Zheng, Po-Xing; Ou, Jheng-Yang; Ting, Chao-Ling; Lin, Yao-Cheng Plant Disease 107(6), 1911-1915
22022DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regenerationChoun-Sea Lin ; Chen-Tran Hsu; Yu-Hsuan Yuan; Po-Xing Zheng; Fu-Hui Wu; Qiao-Wei Cheng; Yu-Lin Wu; Ting-Li Wu; Steven Lin ; Jin-Jun Yue; Ying-Huey Cheng; Shu-I Lin; Ming-Che Shih ; Jen Sheen; Yao-Cheng Lin PLANT PHYSIOLOGY 188(4), 1917-1930
32022Toward automatic plant phenotyping: starting from leaf countingTu, Yi-Lin; Lin, Wei-Yang; Lin, Yao-Cheng Multimedia Tools and Applications 81(9), 11865-11879
42022Whole genome resequencing and complementation tests reveal candidate loci contributing to bacterial wilt (Ralstonia sp.) resistance in tomatoBarchenger, Derek W.; Hsu, Yu-ming; Ou, Jheng-yang; Lin, Ya-ping; Lin, Yao-cheng ; Balendres, Mark Angelo O.; Hsu, Yun-che; Schafleitner, Roland; Hanson, PeterScientific Reports 12(1), 8374
52021Efficient and Economical Targeted Insertion in Plant Genomes via Protoplast RegenerationHsu, Chen-Tran; Yuan, Yu-Hsuan; Lin, Yao-Cheng ; Lin, Steven ; Cheng, Qiao-Wei; Wu, Fu-Hui; Sheen, Jen; Shih, Ming-Che ; Lin, Choun-Sea The CRISPR Journal 4(5), 752-760
62021Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. CitriChien-Jui Huang; Ting-Li Wu; Po-Xing Zheng; Jheng-Yang Ou; Hui-Fang Ni; Yao-Cheng Lin FRONTIERS IN MICROBIOLOGY 12, 731711
72019Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos.Andreia S. Rodrigues; Inês Chaves; Bruno Vasques Costa; Yao-Cheng Lin ; Susana Lopes; Ana Milhinhos; Yves Van de Peer; Célia M. MiguelSCIENTIFIC REPORTS 9, 11327
82019Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccineKatlyn Borgers; Jheng-Yang Ou; Po-Xing Zheng; Petra Tiels; Annelies Van Hecke; Evelyn Plets; Gitte Michielsen; Nele Festjens; Nico Callewaert; Yao-Cheng Lin BMC GENOMICS 20, 561
92019Draft Genome Assembly of the False Spider Mite Brevipalpus yothersiDenise Navia; Valdenice M. Novelli; Stephane Rombauts; Juliana Freitas-Astúa; Renata Santos de Mendonça; Maria Andreia Nunes; Marcos A. Machado; Yao-Cheng Lin ; Phuong Le; Zaichao Zhang; Miodrag Grbić; Nicky Wybouw; Johannes A. J. Breeuwer; Thomas Van Leeuwen; Yves Van de PeerMicrobiology Resource Announcements 8(6), e01563-18
102018Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspenLin, Y.-C. ; Wang, J.; Delhomme, N.; Schiffthaler, B.; Sundström, G.; Zuccolo, A.; Nystedt, B.; Hvidsten, T. R.; de la Torre, A.; Cossu, R. M.; Hoeppner, M. P.; Lantz, H.; Scofield, D. G.; Zamani, N.; Johansson, A.; Mannapperuma, C.; Robinson, K. M.; Mähler, N.; Leitch, I. J.; Pellicer, J.; Park, E.-J.; Van Montagu, M.; Van de Peer, Y.; Grabherr, M.; Jansson, S.; Ingvarsson, P. K.; Street, N. R.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115(46), E10970-E10978
112017Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ipsWingfield, Brenda D.; Berger, Dave K.; Steenkamp, Emma T.; Lim, Hye-Jin; Duong, Tuan A.; Bluhm, Burton H.; de Beer, Z. Wilhelm; De Vos, Lieschen; Fourie, G.; Naidoo, Kershney; Olivier, Nicky; Lin, Yao-Cheng ; Van de Peer, Yves; Joubert, Fourie; Crampton, Bridget G.; Swart, Velushka; Soal, Nicole; Tatham, Catherine; Van der Nest, Magriet A.; Van der Merwe, Nicolaas A.; Van Wyk, Stephanie; Wilken, P. Markus; Wingfield, Michael J.IMA FUNGUS 8(2), 385-396
122017Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem.Christie, N; Myburg, AA; Joubert, F; Murray, SL; Carstens, M; Lin, YC ; Meyer, J; Crampton, BG; Christensen, SA; Ntuli, JF; Wighard, SS; Van de Peer, Y; Berger, DKThe Plant journal : for cell and molecular biology 89(4):746-763
132016The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.Olsen, JL; Rouze, P; Verhelst, B; Lin, YC ; Bayer, T; Collen, J; Dattolo, E; De Paoli, E; Dittami, S; Maumus, F; Michel, G; Kersting, A; Lauritano, C; Lohaus, R; Topel, M; Tonon, T; Vanneste, K; Amirebrahimi, M; Brakel, J; Bostrom, C; Chovatia, M; Grimwood, J; Jenkins, JW; Jueterbock, A; Mraz, A; Stam, WT; Tice, H; Bornberg-Bauer, E; Green, PJ; Pearson, GA; Procaccini, G; Duarte, CM; Schmutz, J; Reusch, TB; Van de Peer, YNature 530(7590), 331-335
142015Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).Delhomme, N; Sundstrom, G; Zamani, N; Lantz, H; Lin, YC ; Hvidsten, TR; Hoppner, MP; Jern, P; Van de Peer, Y; Lundeberg, J; Grabherr, MG; Street, NRPloS one 10(9), e0139080
152015Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays.Ghorbani, S; Lin, YC ; Parizot, B; Fernandez, A; Njo, MF; Van de Peer, Y; Beeckman, T; Hilson, PJournal of experimental botany 66(17), 5257-5269
162015Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families.De La Torre, AR; Lin, YC ; Van de Peer, Y; Ingvarsson, PKGenome biology and evolution 7(4), 1002-1015
172015Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda).Ranade, SS; Lin, YC ; Van de Peer, Y; Garcia-Gil, MRBMC genetics 16, 149
182015The Plant Genome Integrative Explorer Resource: PlantGenIE.org.Sundell, D; Mannapperuma, C; Netotea, S; Delhomme, N; Lin, YC ; Sjodin, A; Van de Peer, Y; Jansson, S; Hvidsten, TR; Street, NRThe New phytologist 208(4), 1149-1156
192014Comparative in silico analysis of EST-SSRsngiosperm and gymnosperm tree genera.Ranade, SS; Lin, YC ; Zuccolo, A; Van de Peer, Y; Garcia-Gil, Mdel RBMC plant biology 14, 220
202014Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations.Lin, YC ; Boone, M; Meuris, L; Lemmens, I; Van, Roy, N; Soete, A; Reumers, J; Moisse, M; Plaisance, S; Drmanac, R; Chen, J; Speleman, F; Lambrechts, D; Van de Peer, Y; Tavernier, J; Callewaert, NNature communications 5, 4767
212014miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns.haves, I.; Lin, Y.-C. ; Pinto-Ricardo, C.; Van de Peer, Y.; Miguel, C.Tree Genetics & Genomes 10, 721-737
222013The biosynthetic gene cluster for sophorolipids: a biotechnological interesting biosurfactant produced by Starmerella bombicola.Van Bogaert, IN; Holvoet, K; Roelants, SL; Li, B; Lin, YC ; Van de Peer, Y; Soetaert, WMolecular microbiology 88(3), 501-509
232013SILAC-based proteome analysis of Starmerella bombicola sophorolipid production.Ciesielska, K; Li, B; Groeneboer, S; Van Bogaert, I; Lin, YC ; Soetaert, W; Van de Peer, Y; Devreese, BJournal of proteome research 12(10), 4376-4392
242013Pan genome of the phytoplankton Emiliania underpins its global distribution.Read, BA; Kegel, J; Klute, MJ; Kuo, A; Lefebvre, SC; Maumus, F; Mayer, C; Miller, J; Monier, A; Salamov, A; Young, J; Aguilar, M; Claverie, JM; Frickenhaus, S; Gonzalez, K; Herman, EK; Lin, YC ; Napier, J; Ogata, H; Sarno, AF; Shmutz, J; Schroeder, D; de Vargas, C; Verret, F; von Dassow, P; Valentin, K; Van de Peer, Y; Wheeler, G; Dacks, JB; Delwiche, CF; Dyhrman, ST; Glockner, G; John, U; Richards, T; Worden, AZ; Zhang, X; Grigoriev, IVNature 499(7457), 209-213
252013The Norway spruce genome sequence and conifer genome evolution.Nystedt, B; Street, NR; Wetterbom, A; Zuccolo, A; Lin, YC ; Scofield, DG; Vezzi, F; Delhomme, N; Giacomello, S; Alexeyenko, A; Vicedomini, R; Sahlin, K; Sherwood, E; Elfstrand, M; Gramzow, L; Holmberg, K; Hallman, J; Keech, O; Klasson, L; Koriabine, M; Kucukoglu, M; Kaller, M; Luthman, J; Lysholm, F; Niittyla, T; Olson, A; Rilakovic, N; Ritland, C; Rossello, JA; Sena, J; Svensson, T; Talavera-Lopez, C; Theissen, G; Tuominen, H; Vanneste, K; Wu, ZQ; Zhang, B; Zerbe, P; Arvestad, L; Bhalerao, R; Bohlmann, J; Bousquet, J; Garcia, Gil, R; Hvidsten, TR; de Jong, P; MacKay, J; Morgante, M; Ritland, K; Sundberg, B; Thompson, SL; Van de Peer, Y; Andersson, B; Nilsson, O; Ingvarsson, PK; Lundeberg, J; Jansson, SNature 497(7451), 579-584
262013Candida bombicola as a platform organism for the production of tailor-made biomolecules.Roelants, SL; Saerens, KM; Derycke, T; Li, B; Lin, YC ; Van de Peer, Y; De Maeseneire, SL; Van Bogaert, IN; Soetaert, WBiotechnology and bioengineering 110(9), 2494-2503
272012GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses.Whitford, R; Fernandez, A; Tejos, R; Perez, AC; Kleine-Vehn, J; Vanneste, S; Drozdzecki, A; Leitner, J; Abas, L; Aerts, M; Hoogewijs, K; Baster, P; De Groodt, R; Lin, YC ; Storme, V; Van de Peer, Y; Beeckman, T; Madder, A; Devreese, B; Luschnig, C; Friml, J; Hilson, PDevelopmental cell 22(3), 678-685
282012Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen.Olson, A; Aerts, A; Asiegbu, F; Belbahri, L; Bouzid, O; Broberg, A; Canback, B; Coutinho, PM; Cullen, D; Dalman, K; Deflorio, G; van Diepen, LT; Dunand, C; Duplessis, S; Durling, M; Gonthier, P; Grimwood, J; Fossdal, CG; Hansson, D; Henrissat, B; Hietala, A; Himmelstrand, K; Hoffmeister, D; Hogberg, N; James, TY; Karlsson, M; Kohler, A; Kues, U; Lee, YH; Lin, YC ; Lind, M; Lindquist, E; Lombard, V; Lucas, S; Lunden, K; Morin, E; Murat, C; Park, J; Raffaello, T; Rouze, P; Salamov, A; Schmutz, J; Solheim, H; Stahlberg, J; Velez, H; de Vries, RP; Wiebenga, A; Woodward, S; Yakovlev, I; Garbelotto, M; Martin, F; Grigoriev, IV; Stenlid, JThe New phytologist 194(4), 1001-1013
292012A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust).Hacquard, S; Joly, DL; Lin, YC ; Tisserant, E; Feau, N; Delaruelle, C; Legue, V; Kohler, A; Tanguay, P; Petre, B; Frey, P; Van de Peer, Y; Rouze, P; Martin, F; Hamelin, RC; Duplessis, SMolecular plant-microbe interactions : MPMI 25(3), 279-293
302011Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine.Chancerel, E; Lepoittevin, C; Le Provost, G; Lin, YC ; Jaramillo-Correa, JP; Eckert, AJ; Wegrzyn, JL; Zelenika, D; Boland, A; Frigerio, JM; Chaumeil, P; Garnier-Gere, P; Boury, C; Grivet, D; Gonzalez-Martinez, SC; Rouze, P; Van de Peer, Y; Neale, DB; Cervera, MT; Kremer, A; Plomion, CBMC genomics 12, 368
312011Obligate biotrophy features unraveled by the genomic analysis of rust fungi.Duplessis, S; Cuomo, CA; Lin, YC ; Aerts, A; Tisserant, E; Veneault-Fourrey, C; Joly, DL; Hacquard, S; Amselem, J; Cantarel, BL; Chiu, R; Coutinho, PM; Feau, N; Field, M; Frey, P; Gelhaye, E; Goldberg, J; Grabherr, MG; Kodira, CD; Kohler, A; Kues, U; Lindquist, EA; Lucas, SM; Mago, R; Mauceli, E; Morin, E; Murat, C; Pangilinan, JL; Park, R; Pearson, M; Quesneville, H; Rouhier, N; Sakthikumar, S; Salamov, AA; Schmutz, J; Selles, B; Shapiro, H; Tanguay, P; Tuskan, GA; Henrissat, B; Van de Peer, Y; Rouze, P; Ellis, JG; Dodds, PN; Schein, JE; Zhong, S; Hamelin, RC; Grigoriev, IV; Szabo, LJ; Martin, FProceedings of the National Academy of Sciences of the United States of America 108(22), 9166-9171
322009Open access to sequence: browsing the Pichia pastoris genome.Mattanovich, D; Callewaert, N; Rouze, P; Lin, YC ; Graf, A; Redl, A; Tiels, P; Gasser, B; De Schutter, KMicrobial cell factories 8, 53
332009Oil bodies and oleosins in Physcomitrella possess characteristics representative of early trends in evolution.Huang, CY; Chung, CI; Lin, YC ; Hsing, YI; Huang, AHPlant physiology 150(3), 1192-1203
342009Genome sequence of the recombinant protein production host Pichia pastoris.De Schutter, K; Lin, YC ; Tiels, P; Van Hecke, A; Glinka, S; Weber-Lehmann, J; Rouze, P; Van de Peer, Y; Callewaert, NNature biotechnology 27(6), 561-566
352008The Rice Annotation Project Database (RAP-DB): 2008 update.Tanaka, T; Antonio, BA; Kikuchi, S; Matsumoto, T; Nagamura, Y; Numa, H; Sakai, H; Wu, J; Itoh, T; Sasaki, T; Aono, R; Fujii, Y; Habara, T; Harada, E; Kanno, M; Kawahara, Y; Kawashima, H; Kubooka, H; Matsuya, A; Nakaoka, H; Saichi, N; Sanbonmatsu, R; Sato, Y; Shinso, Y; Suzuki, M; Takeda, J; Tanino, M; Todokoro, F; Yamaguchi, K; Yamamoto, N; Yamasaki, C; Imanishi, T; Okido, T; Tada, M; Ikeo, K; Tateno, Y; Gojobori, T; Lin, YC ; Wei, FJ; Hsing, YI; Zhao, Q; Han, B; Kramer, MR; McCombie, RW; Lonsdale, D; O’Donovan, CC; Whitfield, EJ; Apweiler, R; Koyanagi, KO; Khurana, JP; Raghuvanshi, S; Singh, NK; Tyagi, AK; Haberer, G; Fujisawa, M; Hosokawa, S; Ito, Y; Ikawa, H; Shibata, M; Yamamoto, M; Bruskiewich, RM; Hoen, DR; Bureau, TE; Namiki, N; Ohyanagi, H; Sakai, Y; Nobushima, S; Sakata, K; Barrero, RA; Sato, Y; Souvorov, A; Smith-White, B; Tatusova, T; An, S; An, G; OOta, S; Fuks, G; Fuks, G; Messing, J; Christie, KR; Lieberherr, D; Kim, H; Zuccolo, A; Wing, RA; Nobuta, K; Green, PJ; Lu, C; Meyers, BC; Chaparro, C; Piegu, B; Panaud, O; Echeverria, MNucleic acids research 36(S1), D1028-D1033
362008The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.Martin, F; Aerts, A; Ahren, D; Brun, A; Danchin, EG; Duchaussoy, F; Gibon, J; Kohler, A; Lindquist, E; Pereda, V; Salamov, A; Shapiro, HJ; Wuyts, J; Blaudez, D; Buee, M; Brokstein, P; Canback, B; Cohen, D; Courty, PE; Coutinho, PM; Delaruelle, C; Detter, JC; Deveau, A; DiFazio, S; Duplessis, S; Fraissinet-Tachet, L; Lucic, E; Frey-Klett, P; Fourrey, C; Feussner, I; Gay, G; Grimwood, J; Hoegger, PJ; Jain, P; Kilaru, S; Labbe, J; Lin, YC ; Legue, V; Le Tacon, F; Marmeisse, R; Melayah, D; Montanini, B; Muratet, M; Nehls, U; Niculita-Hirzel, H; Oudot-Le Secq, MP; Peter, M; Quesneville, H; Rajashekar, B; Reich, M; Rouhier, N; Schmutz, J; Yin, T; Chalot, M; Henrissat, B; Kues, U; Lucas, S; Van de Peer, Y; Podila, GK; Polle, A; Pukkila, PJ; Richardson, PM; Rouze, P; Sanders, IR; Stajich, JE; Tunlid, A; Tuskan, G; Grigoriev, IVNature 452(7183), 88-92
372007A rice phenomics study—phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant populationChern, C. G.; Fan, M. J.; Yu, S. M. ; Hour, A. L.; Lu, P. C.; Lin, Y. C. ; Wei, F. J.; Huang, S. C.; Chen, S.; Lai, M. H.; Tseng, C. S.; Yen, H. M.; Jwo, W. S.; Wu, C. C.; Yang, T. L.; Li, L. S.; Kuo, Y. C.; Li, S. M.; Li, C. P.; Wey, C. K.; Trisiriroj, A.; Lee, H. F.; Hsing, Y. I. C. Plant molecular biology 65(4), 427-438
382007A rice gene activation/knockout mutant resource for high throughput functional genomicsHsing, Y. I.; Chern, C. G.; Fan, M. J.; Lu, P. C.; Chen, K. T.; Lo, S. F.; Sun, P. K.; Ho, S. L.; Lee, K. W.; Wang, Y. C.; Huang, W. L.; Ko, S. S. ; Chen, S.; Chen, J. L.; Chung, C. I.; Lin, Y. C. ; Hour, A. L.; Wang, Y. W.; Chang, Y. C.; Tsai, M. W.; Lin, Y. S.; Chen, Y. C.; Yen, H. M.; Li, C. P.; Wey, C. K.; Tseng, C. S.; Lai, M. H.; Huang, S. C.; Chen, L. J.; Yu, S. M. Plant molecular biology 63(3), 351-364
392007Detection of SNPs between Tainung 67 and Nipponbare rice cultivars.Hour, A.-L.; Lin, Y.-C. ; Li, P.-F.; Chow, T.-Y.; Lu, W.-F.; Wei, F.-J.; Hsing, Y.-I.BOTANICAL STUDIES 48, 243-253
402007Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.Itoh, T; Tanaka, T; Barrero, RA; Yamasaki, C; Fujii, Y; Hilton, PB; Antonio, BA; Aono, H; Apweiler, R; Bruskiewich, R; Bureau, T; Burr, F; Costa de Oliveira, A; Fuks, G; Habara, T; Haberer, G; Han, B; Harada, E; Hiraki, AT; Hirochika, H; Hoen, D; Hokari, H; Hosokawa, S; Hsing, YI; Ikawa, H; Ikeo, K; Imanishi, T; Ito, Y; Jaiswal, P; Kanno, M; Kawahara, Y; Kawamura, T; Kawashima, H; Khurana, JP; Kikuchi, S; Komatsu, S; Koyanagi, KO; Kubooka, H; Lieberherr, D; Lin, YC ; Lonsdale, D; Matsumoto, T; Matsuya, A; McCombie, WR; Messing, J; Miyao, A; Mulder, N; Nagamura, Y; Nam, J; Namiki, N; Numa, H; Nurimoto, S; O’Donovan, C; Ohyanagi, H; Okido, T; Oota, S; Osato, N; Palmer, LE; Quetier, F; Raghuvanshi, S; Saichi, N; Sakai, H; Sakai, Y; Sakata, K; Sakurai, T; Sato, F; Sato, Y; Schoof, H; Seki, M; Shibata, M; Shimizu, Y; Shinozaki, K; Shinso, Y; Singh, NK; Smith-White, B; Takeda, J; Tanino, M; Tatusova, T; Thongjuea, S; Todokoro, F; Tsugane, M; Tyagi, AK; Vanavichit, A; Wang, A; Wing, RA; Yamaguchi, K; Yamamoto, M; Yamamoto, N; Yu, Y; Zhang, H; Zhao, Q; Higo, K; Burr, B; Gojobori, T; Sasaki, TGenome research 17(2), 175-183
412007A repetitive sequence specific to Oryza species with BB genome and abundant in Oryza punctata Kotschy ex SteudCheng, Y. Y.; Fang, S. A.; Lin, Y. C. ; Chung, M. C. Botanical Studies 48, 263-271
422005The map-based sequence of the rice genome.Yao-Cheng Lin ; International Rice Genome Sequencing Project; Takuji SasakiNature 436(7052), 793-800

 

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