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Huang Chien-Jui, Wu Ting-Li, Zheng Po-Xing, Ou Jheng-Yang, Ting Chao-Ling, Lin Yao-Cheng* (2022) Complete Genome Sequence Resource of Pectobacterium colocasium strain F1-1 that Causes Soft Rot Disease of Taro. Plant Disease,
Barchenger Derek W., Hsu Yu-ming, Ou Jheng-yang, Lin Ya-ping, (Lin Yao-cheng), Balendres Mark Angelo O., Hsu Yun-che, Schafleitner Roland, Hanson Peter (2022) Whole genome resequencing and complementation tests reveal candidate loci contributing to bacterial wilt (Ralstonia sp.) resistance in tomato. Scientific Reports, 12(1), 8374
Tu Yi-Lin, Lin Wei-Yang, (Lin Yao-Cheng) (2022) Toward automatic plant phenotyping: starting from leaf counting. Multimedia Tools and Applications, 81(9), 11865-11879
Lin Choun-Sea, Hsu Chen-Tran, Yuan Yu-Hsuan, Zheng Po-Xing, Wu Fu-Hui, Cheng Qiao-Wei, Wu Yu-Lin, Wu Ting-Li, Lin Steven, Yue Jin-Jun, Cheng Ying-Huey, Lin Shu-I, Shih Ming-Che, Sheen Jen, (Lin Yao-Cheng)* (2022) DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration. Plant Physiology, 188(4), 1917-1930
Choun-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* (2022) DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration. Plant Physiology, 188(4): 1917–1930 DOI | News and Views | Cover Image | First Author Profile
Yi-Lin Tu, Wei-Yang Lin & Yao-Cheng Lin (2022) Toward automatic plant phenotyping: starting from leaf counting. Multimedia Tools and Applications, https://doi.org/10.1007/s11042-021-11886-w
Hsu Chen-Tran, Yuan Yu-Hsuan, Lin Yao-Cheng, Lin Steven, Cheng Qiao-Wei, Wu Fu-Hui, Sheen Jen, Shih Ming-Che, Lin Choun-Sea (2021) Efficient and Economical Targeted Insertion in Plant Genomes via Protoplast Regeneration. The CRISPR Journal, 4(5), 752-760 DOI
Chien-Jui Huang*, Ting-Li Wu, Po-Xing Zheng, Jheng-Yang Ou, Hui-Fang Ni and Yao-Cheng Lin* (2021) Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp citri. Frontiers in Microbiology, 12, 2605 DOI
Denise 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 Peer (2019) Draft Genome Assembly of the False Spider Mite Brevipalpus yothersi. Microbiology Resource Announcements, 8(6), e01563-18 DOI
Katlyn Borgers, Jheng-Yang Ou, Po-Xing Zheng, Petra Tiels, Annelies Van Hecke, Evelyn Plets, Gitte Michielsen, Nele Festjens, Nico Callewaert & Yao-Cheng Lin (2019) Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine. BMC Genomics, 20, 561 DOI
Andreia S. Rodrigues, Inês Chaves, Bruno Vasques Costa, Yao-Cheng Lin, Susana Lopes, Ana Milhinhos, Yves Van de Peer & Célia M. Miguel (2019) Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos. SCIENTIFIC REPORTS, 9, 11327
Lin, 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. and Street, N. R. (2018) Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115(46), E10970-E10978 DOI
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 DK (2017) Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem. The Plant journal : for cell and molecular biology, 89(4), 746-763
Zhang, G.-Q., Liu, K.-W., Li, Z., Lohaus, R., Hsiao, Y.-Y., Niu, S.-C., Wang, J.-Y., Lin, Y.-C., Xu, Q., Chen, L.-J., Yoshida, K., Fujiwara, S., Wang, Z.-W., Zhang, Y.-Q., Mitsuda, N., Wang, M., Liu, G.-H., Pecoraro, L., Huang, H.-X., Xiao, X.-J., Lin, M., Wu, X.-Y., Wu, W.-L., Chen, Y.-Y., Bin Chang, S. -, Sakamoto, S., Ohme-Takagi, M., Yagi, M., Zeng, S.-J., Shen, C.-Y., Yeh, C.-M., Luo, Y.-B., Tsai, W.-C., Van de Peer, Y.*, and Liu, Z.-J.* (2017) The Apostasia genome and the evolution of orchids. Nature, 549(7672), 379-383
Huang Chien-Jui, Zheng Po-Xing, Ou Jheng-Yang, Lin Yao-Cheng*, Chen Chao-Ying* (2017) Complete Genome Sequence of Bacillus cereus C1L, a Plant Growth-Promoting Rhizobacterium from the Rhizosphere of Formosa Lily in Taiwan. Genome Announcements, 5(46), e01290-17
Wingfield 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 der Peer Yves, Joubert Fourie, Crampton Bridget G., Swart Velushka, Soal Nicole, Tatham Catherine, Van der Nest Margriet A., Van der Merwe Nicolaas A., van Wyk Stephanie, Wilken P. Markus, Wingfield Michael J.* (2017) Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips. IMA Fungus, 8(2), 385-396
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 Y (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature, 530(7590), 331-335
Sundell D, Mannapperuma C, Netotea S, Delhomme N, Lin YC, Sjodin A, Van de Peer Y, Jansson S, Hvidsten TR, Street NR (2015) The Plant Genome Integrative Explorer Resource: PlantGenIEorg. The New phytologist, 208(4), 1149-1156
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 NR (2015) Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). PloS one, 10(9), e0139080
De La Torre AR, Lin YC, Van de Peer Y, Ingvarsson PK (2015) Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biology and Evolution, 7(4), 1002-1015
Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P (2015) Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. Journal of Experimental Botany, 66(17), 5257-5269
Ranade SS, Lin YC, Van de Peer Y, Garcia-Gil MR (2015) Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda). BMC genetics, 16, 149
haves, I., Lin, Y.-C., Pinto-Ricardo, C., Van de Peer, Y. and Miguel, C. (2014) miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns . Tree Genetics & Genomes, 10, 721-737
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 N (2014) Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations. Nature communications, 5, 4767
Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, Garcia-Gil Mdel R (2014) in aComparative in silico analysis of EST-SSRsngiosperm and gymnosperm tree genera. BMC Plant Biology, 14, 220
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 S (2013) The Norway spruce genome sequence and conifer genome evolution. Nature, 497(7451), 579-584
Van Bogaert IN, Holvoet K, Roelants SL, Li B, Lin YC, Van de Peer Y, Soetaert W (2013) The biosynthetic gene cluster for sophorolipids: a biotechnological interesting biosurfactant produced by Starmerella bombicola. Molecular microbiology, 88(3), 501-509
Ciesielska K, Li B, Groeneboer S, Van Bogaert I, Lin YC, Soetaert W, Van de Peer Y, Devreese B (2013) SILAC-based proteome analysis of Starmerella bombicola sophorolipid production. Journal of proteome research, 12(10), 4376-4392
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 IV (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature, 499(7457), 209-213
Roelants SL, Saerens KM, Derycke T, Li B, Lin YC, Van de Peer Y, De Maeseneire SL, Van Bogaert IN, Soetaert W (2013) Candida bombicola as a platform organism for the production of tailor-made biomolecules. Biotechnology and bioengineering, 110(9), 2494-2503
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 J (2012) Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. The New phytologist, 194(4), 1001-1013
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 P (2012) GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental cell, 22(3), 678-685
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 S (2012) A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust). Molecular plant-microbe interactions : MPMI, 25(3), 279-293
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 F (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proceedings of the National Academy of Sciences of the United States of America, 108(22), 9166-9171
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 C (2011) Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Genomics, 12, 368
Mattanovich D, Callewaert N, Rouze P, Lin YC, Graf A, Redl A, Tiels P, Gasser B, De Schutter K (2009) Open access to sequence: browsing the Pichia pastoris genome. Microbial cell factories, 8, 53
Huang CY, Chung CI, Lin YC, Hsing YI, Huang AH (2009) Oil bodies and oleosins in Physcomitrella possess characteristics representative of early trends in evolution. Plant Physiology, 150(3), 1192-1203
De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, Rouze P, Van de Peer Y, Callewaert N (2009) Genome sequence of the recombinant protein production host Pichia pastoris. Nature biotechnology, 27(6), 561-566
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 M (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic acids research, 36(S1), D1028-D1033
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 IV (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature, 452(7183), 88-92
Hour, A.-L., Lin, Y.-C., Li, P.-F., Chow, T.-Y., Lu, W.-F., Wei, F.-J., Hsing, Y.-I. (2007) Detection of SNPs between Tainung 67 and Nipponbare rice cultivars . Botanical Studies, 48, 243-253
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 T (2007) Curated genome annotation of Oryza sativa ssp japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research, 17(2), 175-183
Chern CG, Fan MJ, Yu SM, Hour AL, Lu PC, Lin YC, Wei FJ, Huang SC, Chen S, Lai MH, Tseng CS, Yen HM, Jwo WS, Wu CC, Yang TL, Li LS, Kuo YC, Li SM, Li CP, Wey CK, Trisiriroj A, Lee HF, Hsing YI (2007) A rice phenomics study--phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. Plant Molecular Biology, 65(4), 427-438
Hsing YI, Chern CG, Fan MJ, Lu PC, Chen KT, Lo SF, Sun PK, Ho SL, Lee KW, Wang YC, Huang WL, Ko SS, Chen S, Chen JL, Chung CI, Lin YC, Hour AL, Wang YW, Chang YC, Tsai MW, Lin YS, Chen YC, Yen HM, Li CP, Wey CK, Tseng CS, Lai MH, Huang SC, Chen LJ, Yu SM (2007) A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Molecular Biology, 63(3), 351-364
Cheng, Y.-Y., Fang, S.-A., Lin, Y.-C., Chung, M.-C. (2007) A repetitive sequence specific to Oryza species with BB genome and abundant in Oryza punctata. Botanical Studies, 48, 263-272
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436(7052), 793-800
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