Yao-Cheng Lin

Staff Scientist
(Group member from 2006 until 2016)


+ 32 (0) 9 33 13 821

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

CV

Birth: 8 July 1976, Tainan, Taiwan

November 2011: Staff Scientist, VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium.

April 2011 – October 2011: Postdoctoral researcher, VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium.

November 2006 – March 2011: Ph.D. studies, ‘Annotation and comparative analysis of fungal genomes – a hitchhiker’s guide to genomics’. Promoter: Prof. Yves Van de Peer, VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium.

July 2002 – October 2006: Research Assistant, Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.

July 1999 – June 2001: Master studies, Institute of Anatomy and Cell Biology, National Yang-Ming University, Taipei, Taiwan.

July 1994 – June 1999: Bachelor studies, Department of Agronomy, National Taiwan University, Taipei, Taiwan.

Service as reviewer: BMC Genomics, BMC Plant Biology, Current Plant Biology, Bioinformatics, Frontiers in Plant Science, Genomics, Genome Biology and Evolution, PLOS One, The Plant Journal, Tree Genetics and Genomics and European Conference on Computational Biology (ECCB 2011, 2012 and 2014)

Research

Gene Prediction and Computational Genomics

Starting from the International Rice Genome Sequencing Project, I have been actively involved in more than a dozen (inter-)national genome projects serving as an expert annotator and provide high quality computational genome annotation for research communities. The advance of sequencing technologies posts a great challenge in current gene prediction workflow and my main interest is integrating large scale genomics data into a next generation genome annotation platform to provide a high quality structure and functional annotation.

Computational genomics is a technology driven field. I am interesting in developing and applying high throughout sequencing technologies together with large scale, genome wide analysis methods to revel the complex interaction between biological systems.

Papers

(31) Christie, K.R., Myburg, A.A., Joubert, Y., Murray, S.L., Carstens, M., Lin, Y.-C., Meyer, J., Crampton, B.G., Christensen, S.A., Ntuli, J.F., Wighard, S.S., Van de Peer, Y., Berger, D.K. (2016) Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem. The Plant Journal (In Press).

(30) Olsen, J.L., Rouzé, P., Verhelst, B., Lin, Y.-C., Bayer, T., Collen, J., Dattolo, E., De Paoli, E., Dittami, S., Maumus, F., Michel, G., Kersting, A.R., Lauritano, C., Lohaus, R., T?pel, M., Tonon, T., Vanneste, K., Amirebrahimi, M., Brakel, J., Bostr?m, C., Chovatia, M., Grimwood, J., Jenkins, B., J?terbock, A., Mraz, A., Stam, W.T., Tice, H., Bornberg-Bauer, E., Green, P.J., Pearson, G.A., Procaccini, G., Duarte, C.M., Schmutz, J., Reusch, T.B.H., Van de Peer, Y. (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 530(7590):331-5.

(29) Lin, Y.-C., Van de Peer, Y., García-Gil, M. (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) Sonali Sachin Ranade. BMC Genetics 16(1):149.

(28) Delhomme, N., Sundström, G., Zamani, N., Lantz, H., Lin, Y.-C., R. Hvidsten, T., P. Höppner, M., Jern, P., Van de Peer, Y., Lundeberg, J., G. Grabherr, M., Street, N.R. (2015) Serendipitous Meta-Transcriptomics: the fungal community of Norway spruce (Picea abies). PLoS One 10(9):e0139080.

(27) Sundell, D., Mannapperuma, C., Netotea, S., Delhomme, N., Lin, Y.-C., Sjödin, A., Van de Peer, Y., Jansson, S., Hvidsten, T. R., Street, N. R. (2015) The Plant Genome Integrative Explorer Resource: PlantGenIE.org. New Phytol. 208(4):1149-56.

(26) Ghorbani, S., Lin, Y.-C., Parizot, B., Fernandez, A., Fransiska Njo, M., 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):5257-69.

(25) De La Torre, A.R., Lin, Y.-C., Van de Peer, Y., Ingvarsson, P.K. (2015) Genome-wide analysis reveals diverged patterns of codon bias, gene expression and rates of sequence evolution in Picea gene families. Genome Biol. Evol. 7(4):1002-1015.

(24) Lin, Y.-C., Boone, M., Meuris, L., Lemmens, K., Van Roy, N., Soete, A., Reumers, J., Moisse, M., Plaisance, S., Drmanac, R., Chen, J., Speleman, GF., Lambrechts, A., Van de Peer, Y., Tavernier, J., Callewaert, L. (2014) Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations. Nature Comm. 5:4767.

(23) Ranade, S., Lin, Y.-C., Zuccolo, A., Van de Peer, Y., García-Gil, M. (2014) Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC Plant Biol. 14:220.

(22) Chaves, I., Lin, Y.-C., Pinto Ricardo, C., Van de Peer, Y., 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(3):721-737.

(21) Ciesielska, K., Li, B., Groeneboer, S., Van Bogaert, M., Lin, Y.-C., Soetaert, W., Van de Peer, Y., Devreese, B. (2013) SILAC-based proteome analysis of Starmerella bombicola sophorolipid production. Journal of Proteome Research 12(10):4376-92.

(20) Read, B. A., Kegel, J., Klute, M. J., Kuo, Y.-C., Lefebvre, S. C., Maumus, F., Mayer, K., Miller, G., Monier, A., Salamov, A., Young, N.D., Aguilar, ., Aguilar, ., Claverie, J., Frickenhaus, S., Gonzalez, A., Herman, E. K., Lin, Y.-C., Napier, J., Ogata, H., Sarno, A. F., Schmutz, J., Schroeder, D., de Vargas, C., Vérret, F., von Dassow, P., Valentin, K., Van de Peer, Y., Rouzé, P., Wheeler, G., Allen, A. E., Bidle, K., Borodovsky, M., Bowler, C., Brownlee, C., Mark Cock, J., Elias, M., Gladyshev, V. N., Groth, M., Groth, M., Guda, C., Hadaegh, A., Iglesias-Rodriguez, D., Jenkins, B., Jones, B. M., Leese, F., Lobanov, A., Lawson, T., Lindquist, E., Marsh, M. E., Lomsadze, A., Mueller-Roeber, B., Lucas, S., Malik, S.-B., Pagarete, A., Mock, T., Probert, I., Parker, M.S., Quesneville, H., Raines, C., Rensing, S.A., Mauricio Riano-Pachon, D., Richier, S., Rokitta, S., Shiraiwa, Y., Soanes, D. M., van der Giezen, M., Wahlund, T. M., Williams, C., Wilson, W., Wolfe, K., Wurch, L. L., Dacks, J. B., Delwiche, C. F., Dyhrman, S. T., Glöckner, G., John, U., Richards, T., Worden, A. Z., Zhang, J., V. Grigoriev, I. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499(7457):209-13.

(19) Nystedt, B., Street, N. R., Zuccolo, A., Lin, Y.-C., Wetterbom, A., Vezzi, A., Scofield, D. G., Delhomme, N., Alexeyenko, A., Giacomello, S., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstand, M., Gramzow, L., Holmberg, K., Hällman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Käller, M., Luthman, J., Lysholm, F., Olson, A., Niittylä, T., Ritland, K., Rilakovic, N., Rosselló, J. A., Sena, J., Svensson, T., Talavera-López, C., Theißen, G., Vanneste, K., Tuominen, H., Zhang, J., Wu, Z., Zerbe, P., Bhalerao, R.P., Bohlmann, J., Arvestad, L., Bousquet, J., Garcia Gil, R., de Jong, P.J., Hvidsten, T. R., MacKay, J., Ritland, K., Morgante, M., Sundberg, B., Van de Peer, Y., Lee Thompson, S., Nilsson, O., Andersson, B., Lundeberg, J., Jansson, S. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497(7451):579-84.

(18) Van Bogaert, M., Holvoet, K., Roelants, S. L.K.W, Li, B., Lin, Y.-C., 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):501-9.

(17) Roelants, S. L.K.W, Saerens, K.M., Derycke, T., Li, B., Lin, Y.-C., Van de Peer, Y., De Maeseneire, S.L., Van Bogaert, M., Soetaert, W. (2013) Candida bombicola as a platform organism for the production of tailor-made biomolecules. Biotechnol. Bioeng. 110(9):2494-503.

(16) Olson, A., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., Canbäck, B., Coutinho, P.M., Cullen, D., Dalman, K., Deflorio, G., van Diepen, L., Dunand, C., Duplessis, S., Durling, M., Gonthier, P., Grimwood, J., Gunnar Fossdal, C., Hansson, D., Henrissat, B., Hietala, A., Himmelstrand, K., Hoffmeister, D., Hogberg, N., James, T., Karlsson, J., Kohler, A., Kües, U., Lee, Y., Lin, Y.-C., Lind, M., Lindquist, E., Lombard, V., Lucas, S., Lunden, K., Morin, E., Murat, C., Park, R., Raffaello, T., Rouzé, P., Salamov, A., Schmutz, J., Solheim, H., Stahlberg, J., Velez, M., de Vries, R., Wiebenga, A., Woodward, S., Yakovlev, I., Garbelotto, M., Martin, F., Grigoriev, I., Stenlid, J. (2012) Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol. 194, 1001-13.

(15) Whitford, R., Fernandez, A., Tejos, R., Cuellar Perez, A., Kleine-Vehn, J., Vanneste, S., Drozdzecki, A., Leitner, J., Abas, L., Aerts, M., Hoogewijs, K., Baster, P., De Groodt, R., Lin, Y.-C., 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. Dev. Cell 22,678-85.

(14) Hacquard, S., Joly, D., Lin, Y.-C., Tisserant, E., Feau, N., Delaruelle, C., Legué, V., Kohler, A., Tanguay, P., Petre, B., Frey, P., Van de Peer, Y., Rouzé, P., Martin, F., Hamelin, R., Duplessis, S. (2012) A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici- populina (poplar leaf rust). Mol. Plant Microbe In. 25(3):279-93.

(13) Chancerel, E., Lepoittevin, C., Le Provost, G., Lin, Y.-C., Pablo Jaramillo-Correa, J., J Eckert, A., L Wegrzyn, J., Zelenika, D., Boland, A., Frigerio, J., Chaumeil, P., Garnier-Géré, P., Boury, C., Grivet, D., C González-Martínez, S., Rouzé, P., Van de Peer, Y., B Neale, D., T Cervera, M., 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.

(12) Duplessis, S., A. Cuomo, C., Lin, Y.-C., Aerts, A., Tisserant, E., Veneault-Fourrey, C., L. Joly, D., Hacquard, S., Amselem, J., L. Cantarel, B., Chiu, C.-H., Couthinho, P., Feau, N., Field, M., Frey, P., Gelhaye, E., Goldberg, J., Grabherr, M., D. Kodira, C., Kohler, A., Kües, U., A. Lindquist, E., Lucas, S., Mago, R., Mauceli, E., Morin, E., Murat, C., L. Pangilinan, J., Park, R., Pearson, M., Quesneville, H., Rouhier, N., Sakthikumar, S., A. Salamov, A., Schmutz, J., Selles, B., Shapiro, H.J., Tangay, P., Henrissat, B., Van de Peer, Y., Rouzé, P., G. Ellis, J., N. Dodds, P., E. Schein, J., Zhong, S., C. Hamelin, R., V. Grigoriev, I., J. Szabon, L., Martina, F. (2011) Obligate Biotrophy Features Unraveled by the Genomic Analysis of Rust Fungi. Proc. Natl. Acad. Sci. USA 108(22):9166-71.

(11) Mattanovich, D., Callewaert, L., Rouzé, P., Lin, Y.-C., 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.

(10) Huang, C-Y., Chung, C., Lin, Y.-C., Hsing, Y., Huang, A. (2009) Oil Bodies and Oleosins in Physcomitrella Possess Characteristics Representative of Early Trends in Evolution. Plant Physiol. 150(3):1192-203.

(9) De Schutter, K., Lin, Y.-C., Tiels, P., Van Hecke, A., Glinka, S., Weber-Lehmann, J., Rouzé, P., Van de Peer, Y., Callewaert, L. (2009) Genome sequence of the recombinant protein production host Pichia pastoris, a methylotrophic yeast. Nature Biotechnology 27(6):561-6.

(8) Martin, F., Aerts, A., Ahrén, D., Brun, A., Duchaussoy, F., Gibon, J., Kohler, A., Lindquist, E., Pereda, V., Salamov, A., Shapiro, H.J., Wuyts, J., Blaudez, D., Buée, M., Brokstein, P., Canbäck, B., Cohen, D., Courty, P.E., Coutinho, P., Danchin, E.G.J., Delaruelle, C., Detter, J., Deveau, A., DiFazio, S., Duplessis, S., Fraissinet-Tachet, L., Lucic, E., Frey-Klett, P., Fourrey, C., Feussner, I., Gay, G., Gérard, J., Grimwood, J., Hoegger, P.J., Jain, P., Kilaru, S., Labbé, J., Lin, Y.-C., Legué, V., F LeTacon, ., Marmeisse, R., Melayah, D., Montanini, B., Muratet, M., Nehls, U., Niculita-Hirzel, H., Oudot-LeSecq, M.P., Peter, G., Quesneville, H., Rajashekar, B., Reich, M., Rouhier, N., Schmutz, J., Yin, T., Chalot, M., Henrissat, B., Kües, U., Lucas, S., Van de Peer, Y., Podila, G., Polle, A., Pukkila, PJ., Richardson, P., Rouzé, P., Sanders, I., Stajich, J.E., Tunlid, A., Tuskan, G., Grigoriev, I. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452(7183):88-92.

(7) Tanaka, T., Antonio, B., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, H., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, T., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, S., Shinso, Y., Suzuki, Y., 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, Y.-C., Wei, F.-J., Hsing, Y., Zhao, Q., Han, B., Kramer, M.R., McCombie, R.W., Lonsdale, D., O'Donovan, C., Whitfield, E.J., Apweiler, R., Koyanagi, K., Khurana, J., Raghuvanshi, S., Singh, N., Tyagi, A., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R., Hoen, D., Bureau, T., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R., Sato, S., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., OOta, S., Fuks, G., Fuks, G., Messing, J., Christie, K.R., Lieberherr, D., Kim, J.R., Zuccolo, A., Wing, R., Nobuta, K., Green, P.J., Lu, C., Meyers, B.C., Chaparro, C., Piegu, B., Panaud, O., Echeverria, M. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36(Database issue):D1028-33.

(6) * Hour, A., * Lin, Y.-C., Li, P.-F., Chow, T.-Y., Lu, W.-F., Wei, F.-J., Hsing, Y. (2007) Detection of SNPs between Tainung 67 and Nipponbare rice cultivars. Bot. Stud. 48:243-53. *contributed equally

(5) Chern, C., Fan, M.-J., Yu, S.-M., Hour, A., Lu, P., Lin, Y.-C., Wei, F.-J., Huang, S.-C., Chen, S., Lai, M.-H., Tseng, C., Yen, H., Jwo, W.-S., Wu, C.-C., Yang, T.-L., Li, L.-S., Kuo, Y.-C., Li, S.-M., Li, C.-P., Wey, C., Trisiriroj, A., Lee, H.-F., Hsing, Y. (2007) A rice phenomics study-phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population. Plant Mol Biol 65(4):427-38.

(4) Cheng, Y.-Y., Fang, S.-A., Lin, Y.-C., Chung, C. (2007) A repetitive sequence specific to Oryza species with BB genome and abundant in Oryza punctata Kotschy ex Steud. Bot. Stud. 48:263-72.

(3) Hsing, Y., Chern, C., Toffano, C., Lu, P., Chen, K., Lo, S., Sundaresan, V., Ho, S., Lee, K., Wang, X., Huang, W., Ko, S., Chen, J., Chen, J., Chung, C., Lin, Y.-C., Hour, A., Wang, X., Chang, Y., Tsai, C., Lin, Y., Chen, Y., Yen, H., Li, C., Wey, C., Tseng, C., Nicolai, S., Huang, W., Chen, L., Feldblyum, T. (2007) A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol. Biol. 63(3):351-64.

(2) Itoh, T., Tanaka, T., Barrero, R., Yamasaki, C., Fujii, Y., Hilton, P., Antonio, B., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., Oliveira, A., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, T., Kawamura, T., Kawashima, H., Khurana, J., Kikuchi, S., Komatsu, S., Koyanagi, K., Kubooka, H., Lieberherr, D., Lin, Y.-C., Lonsdale, D., Matsumoto, T., Matsuya, A., W. McCombie, R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Putnam, N., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., OOta, S., Osato, N., Palmer, L., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, S., Sato, S., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N., Smith-White, B., Takeda, J., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A., Vanavichit, A., Wang, X., Wing, R., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Feldblyum, T., Zhang, J., 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 Res. 17(2):175-83.

(1) Lin, Y.-C. (2005) A map-based sequence of the rice genome. Nature 436(7052):793-800.











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