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Lukas Mueller

Lukas Mueller
Lukas Mueller
Assistant Professor
Office/Lab: 221
lam87@cornell.edu
Office: 607 255 6557
Lab:

Research Summary

Research Summary

My interests are in the field of bioinformatics and genomics, and in particular genome sequencing, structural and functional annotation, biochemical pathways, comparative genomics, data presentation and visualization, ontology development, and biological databases. I am coordinating the SOL Genomics Network (SGN), a site for genome data of Solanaceae species such as tomato, potato and pepper, and am involved in the tomato genome sequencing project.

Previously, I was involved with the floral genome project and have worked with the Arabidopsis Information Resource (TAIR), where I was involved in Arabidopsis genome annotation, TAIR tool and database development, and projects such as AraCyc, Pubsearch, and others.

Sol Genomics

DNA Sequence Puzzle

Selected Publications

Selected Publications

View All Publications    |    All papers on PubMed

Bombarely, A., Rosli, H.G., Vrebalov, J., Moffett, P., Mueller, L.A. and Martin, G.B. 2012. A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Molecular plant-microbe interactions 25: 1523-1530

Bombarely, A., Edwards, K.D., Sanchez-Tamburrino, J. and Mueller, L.A. 2012. Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective. Bmc Genomics 13:

Caspi, R., Altman, T., Dreher, K., Fulcher, C.A., Subhraveti, P., Keseler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A., Ong, Q., Paley, S., Pujar, A., Shearer, A.G., Travers, M., Weerasinghe, D., Zhang, P.F. and Karp, P.D. 2012. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research 40: D742-D753

Cai, D.Y., Rodriguez, F., Teng, Y.W., Ane, C., Bonierbale, M., Mueller, L.A. and Spooner, D.M. 2012. Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). Bmc Evol Biol 12: 70

Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B.K., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, L.A., Zhao, H., He, H., Zhang, Y., Zhang, Z., Huang, S., Tan, T., Pang, E., Lin, K., Hu, Q., Kuang, H., Ni, P., Wang, B., Liu, J., Kou, Q., Hou, W., Zou, X., Jiang, J., Gong, G., Klee, K., Schoof, H., Huang, Y., Hu, X., Dong, S., Liang, D., Wang, J., Wu, K., Xia, Y., Zhao, X., Zheng, Z., Xing, M., Liang, X., Huang, B., Lv, T., Wang, J., Yin, Y., Yi, H., Li, R., Wu, M., Levi, A., Zhang, X., Giovannoni, J.J., Wang, J., Li, Y., Fei, Z. and Xu, Y. 2012. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45: 51-58

Lopez-Casado, G., Covey, P.A., Bedinger, P.A., Mueller, L.A., Thannhauser, T.W., Zhang, S., Fei, Z.J., Giovannoni, J.J. and Rose, J.K.C. 2012. Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case. Proteomics 12: 761-774

Merk, H.L., Yarnes, S.C., Van Deynze, A., Tong, N.K., Menda, N., Mueller, L.A., Mutschler, M.A., Loewen, S.A., Myers, J.R. and Francis, D.M. 2012. Trait diversity and potential for selection indices based on variation among regionally adapted processing tomato germplasm. J Am Soc Hortic Sci 137: 427-437

Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y., Shibata, D., Aoki, K., Egholm, M., Knight, J., Bogden, R., Li, C.B., Shuang, Y., Xu, X., Pan, S.K., Cheng, S.F., Liu, X., Ren, Y.Y., Wang, J., Albiero, A., Dal Pero, F., Todesco, S., Van Eck, J., Buels, R.M., Bombarely, A., Gosselin, J.R., Huang, M.Y., Leto, J.A., Menda, N., Strickler, S., Mao, L.Y., Gao, S., Tecle, I.Y., York, T., Zheng, Y., Vrebalov, J.T., Lee, J., Zhong, S.L., Mueller, L.A., Stiekema, W.J., Ribeca, P., Alioto, T., Yang, W.C., Huang, S.W., Du, Y.C., Zhang, Z.H., Gao, J.C., Guo, Y.M., Wang, X.X., Li, Y., He, J., Li, C.Y., Cheng, Z.K., Zuo, J.R., Ren, J.F., Zhao, J.H., Yan, L.H., Jiang, H.L., Wang, B., Li, H.S., Li, Z.J., Fu, F.Y., Chen, B.T., Han, B., Feng, Q., Fan, D.L., Wang, Y., Ling, H.Q., Xue, Y.B.A., Ware, D., McCombie, W.R., Lippman, Z.B., Chia, J.M., Jiang, K., Pasternak, S., Gelley, L., Kramer, M., Anderson, L.K., Chang, S.B., Royer, S.M., Shearer, L.A., Stack, S.M., Rose, J.K.C., Xu, Y.M., Eannetta, N., Matas, A.J., McQuinn, R., Tanksley, S.D., Camara, F., Guigo, R., Rombauts, S., Fawcett, J., Van de Peer, Y., Zamir, D., Liang, C.B., Spannagl, M., Gundlach, H., Bruggmann, R., Mayer, K., Jia, Z.Q., Zhang, J.H., Ye, Z.B.A., Bishop, G.J., Butcher, S., Lopez-Cobollo, R., Buchan, D., Filippis, I., Abbott, J., Dixit, R., Singh, M., Singh, A., Pal, J.K., Pandit, A., Singh, P.K., Mahato, A.K., Dogra, V., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Causse, M., Rothan, C., Schiex, T., Noirot, C., Bellec, A., Klopp, C., Delalande, C., Berges, H., Mariette, J., Frasse, P., Vautrin, S., Zouine, M., Latche, A., Rousseau, C., Regad, F., Pech, J.C., Philippot, M., Bouzayen, M., Pericard, P., Osorio, S., del Carmen, A.F., Monforte, A., Granell, A., Fernandez-Munoz, R., Conte, M., Lichtenstein, G., Carrari, F., De Bellis, G., Fuligni, F., Peano, C., Grandillo, S., Termolino, P., Pietrella, M., Fantini, E., Falcone, G., Fiore, A., Giuliano, G., Lopez, L., Facella, P., Perrotta, G., Daddiego, L., Bryan, G., Orozco, M., Pastor, X., Torrents, D., van Schriek, K.N.V.M.G.M., Feron, R.M.C., van Oeveren, J., de Heer, P., daPonte, L., Jacobs-Oomen, S., Cariaso, M., Prins, M., van Eijk, M.J.T., Janssen, A., van Haaren, M.J.J., Jo, S.H., Kim, J., Kwon, S.Y., Kim, S., Koo, D.H., Lee, S., Hur, C.G., Clouser, C., Rico, A., Hallab, A., Gebhardt, C., Klee, K., Jocker, A., Warfsmann, J., Gobel, U., Kawamura, S., Yano, K., Sherman, J.D., Fukuoka, H., Negoro, S., Bhutty, S., Chowdhury, P., Chattopadhyay, D., Datema, E., Smit, S., Schijlen, E.W.M., van de Belt, J., van Haarst, J.C., Peters, S.A., van Staveren, M.J., Henkens, M.H.C., Mooyman, P.J.W., Hesselink, T., van Ham, R.C.H.J., Jiang, G.Y., Droege, M., Choi, D., Kang, B.C., Kim, B.D., Park, M., Kim, S., Yeom, S.I., Lee, Y.H., Choi, Y.D., Li, G.C., Gao, J.W., Liu, Y.S., Huang, S.X., Fernandez-Pedrosa, V., Collado, C., Zuniga, S., Wang, G.P., Cade, R., Dietrich, R.A., Rogers, J., Knapp, S., Fei, Z.J., White, R.A., Thannhauser, T.W., Giovannoni, J.J., Botella, M.A., Gilbert, L., Gonzalez, R., Goicoechea, J.L., Yu, Y., Kudrna, D., Collura, K., Wissotski, M., Wing, R., Schoof, H., Meyers, B.C., Gurazada, A.B., Green, P.J., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A.K., Dalmay, T., Mohorianu, I., Walts, B., Chamala, S., Barbazuk, W.B., Li, J.P., Guo, H., Lee, T.H., Wang, Y.P., Zhang, D., Paterson, A.H., Wang, X.Y., Tang, H.B., Barone, A., Chiusano, M.L., Ercolano, M.R., D'Agostino, N., Di Filippo, M., Traini, A., Sanseverino, W., Frusciante, L., Seymour, G.B., Elharam, M., Fu, Y., Hua, A., Kenton, S., Lewis, J., Lin, S.P., Najar, F., Lai, H.S., Qin, B.F., Qu, C.M., Shi, R.H., White, D., White, J., Xing, Y.B., Yang, K.Q., Yi, J., Yao, Z.Y., Zhou, L.P., Roe, B.A., Vezzi, A., D'Angelo, M., Zimbello, R., Schiavon, R., Caniato, E., Rigobello, C., Campagna, D., Vitulo, N., Valle, G., Nelson, D.R., De Paoli, E., Szinay, D., de Jong, H.H., Bai, Y.L., Visser, R.G.F., Lankhorst, R.M.K., Beasley, H., McLaren, K., Nicholson, C., Riddle, C., Gianese, G. and Consortium, T.G. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641

Strickler, S.R., Bombarely, A. and Mueller, L.A. 2012. Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am J Bot 99: 257-266

Privat, I., Bardil, A., Gomez, A.B., Severac, D., Dantec, C., Fuentes, I., Mueller, L., Joet, T., Pot, D., Foucrier, S., Dussert, S., Leroy, T., Journot, L., de Kochko, A., Campa, C., Combes, M.C., Lashermes, P. and Bertrand, B, . 2011. The 'PUCE CAFE' project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits. Bmc Genomics 12: 5

Jung, S., Menda, N., Redmond, S., Buels, R.M., Friesen, M., Bendana, Y., Sanderson, L.A., Lapp, H., Lee, T., MacCallum, B., Bett, K.E., Cain, S., Clements, D., Mueller, L.A. and Main, D. 2011. The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. Database 0: bar051

Bombarely, A., Menda, N., Tecle, I.Y., Buels, R.M., Strickler, S., Fischer-York, T., Pujar, A., Leto, J., Gosselin, J. and Mueller, L.A. 2011. The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res 39: D1149-1155

Edwards, K.D., Bombarely, A., Story, G.W., Allen, F., Mueller, L.A., Coates, S.A. and Jones, L. 2010. TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics 11: 142

De Kochko, A., Akaffou, S., Andrade, A.C., Campa, C., Crouzillat, D., Guyot, R., Hamon, P., Ming, R., Mueller, L.A., Poncet, V., Tranchant-Dubreuil, C. and Hamon, S. 2010. Advances in Coffea genomics. Advances in Botanical Research 53: 23-63

Caspi, R., Altman, T., Dale, J.M., Dreher, K., Fulcher, C.A., Gilham, F., Kaipa, P., Karthikeyan, A.S., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A., Paley, S., Popescu, L., Pujar, A., Shearer, A.G., Zhang, P. and Karp, P.D. 2010. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research 38: D473-D479

Scaria, J., Ponnala, L., Janvilisri, T., Yan, W.W., Mueller, L.A. and Chang, Y.F. 2010. Analysis of Ultra Low Genome Conservation in Clostridium difficile. Plos One 5: e15147

Tecle, I.Y., Menda, N., Buels, R.M., van der Knaap, E. and Mueller, L.A. 2010. solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. BMC Bioinformatics 11: 525

Zhang, P.F., Dreher, K., Karthikeyan, A., Chi, A., Pujar, A., Caspi, R., Karp, P., Kirkup, V., Latendresse, M., Lee, C., Mueller, L.A., Muller, R. and Rhee, S.Y. 2010. Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiology 153: 1479-1491

Mueller, L.A., Lankhorst, R.K., Tanksley, S.D., Giovannoni, J.J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A.A., Menda, N., Tecle, I.Y., Bombarely, A., Stack, S., Royer, S.M., Chang, S.-B., Shearer, L.A., Kim, B.D., Jo, S.-H., Hur, C.-G., Choi, D., Li, C.-B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G.B., Bishop, G.J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A.U., Kumar, R., Gupta, V., Sharma, A.K., Khurana, P., Khurana, J.P., Tyagi, A., Sarita, Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I.A., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., Szinay, D., de Jong, H., Peters, S., van Staveren, M., Datema, E., Fiers, M.W.E.J., van Ham, R.C.H.J., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M.A., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, N., Chiusano, M.L., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jcker, A., Bruggmann, R., Spannagl, M., Mayer, K.X.F., Guig, R., Camara, F., Rombauts, S., Fawcett, J.A., Van de Peer, Y., Knapp, S., Zamir, D. and Stiekema, W. 2009. A snapshot of the emerging tomato genome sequence. The Plant Genome 2: 78-92

Mazourek, M., Pujar, A., Borovsky, Y., Paran, I., Mueller, L. and Jahn, M.M. 2009. A dynamic interface for capsaicinoid systems biology. Plant Physiology 150: 1806-1821

Menda, N., Buels, R.M., Tecle, I. and Mueller, L.A. 2008. A community-based annotation framework for linking Solanaceae genomes with phenomes. Plant Physiol 147: 1788-1799

Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD. 2006. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics. 2006 Nov; 174: 1407-20

Carlson JE, Leebens-Mack JH, Wall PK, Zahn LM, Mueller LA, Landherr LL, Hu Y, Ilut DC, Arrington JM, Choirean S, Becker A, Field D, Tanksley SD, Ma H, dePamphilis CW. 2006. EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot. Plant Mol Biol. 2006 Oct; 62: 351-69

Mueller LA, Steven D. Tanksley , Jim J. Giovannoni , Joyce van Eck , Stephen Stack, Doil Choi, Byung Dong Kim, Mingsheng Chen, Zhukuan Cheng, Chuanyou Li, Hongqing Ling, Yongbiao Xue, Graham Seymour, Gerard Bishop, Glenn Bryan, Rameshwar Sharma, Jiten Khurana, Akhilesh Tyagi, Debasis Chattopadhyay, Nagendra K. Singh, Willem Stiekema, P. Lindhout, Taco Jesse, Rene Klein Lankhorst, Mondher Bouzayen, Daisuke Shibata, Satoshi Tabata, Antonio Granell, Miguel A. Botella, Giovanni Giuliano, Luigi Frusciante, Mathilde Causse and Dani Zamir. 2005. The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL). Comparative and Functional Genomics 6: 153 -158

Lin C, Mueller LA, Carthy JM, Crouzillat D, Petiard V, Tanksley SD. 2005. Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet. ?:p 0: 1-17 [PMID: 16273343]

Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY. 2005. MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol 138: 27-37

Markus Krummenacker, Suzanne M. Paley, Lukas A. Mueller, Thomas Yan, Peter D. Karp. 2005. Querying and computing with BioCyc databases. Bioinformatics 21: 3454-3455

Wang Y, van der Hoeven RS, Nielsen R, Mueller LA, Tanksley SD. 2005. Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor Appl Genet 6: 1-13

Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee SY. 2005. PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res 33: (Web Server issue):W262-6. PMID: 15980466

Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Solow TM, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo MJ, Frohlich MW, Perl-Treves R, Schlarbaum SE, Bliss BJ, Zhang X, Tanksley SD, Oppenheimer DG, Soltis PS, Ma H, DePamphilis CW, Leebens-Mack JH. 2005. Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol. 30; 5: 5

Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst EV, Keyder ER, Menda N, Zamir D, Tanksley SD. 2005. The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 138: 1310-7

Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, Rhee SY. 2004. Related Articles, Links Abstract Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol Jun; 135: 745-55. Epub 2004 Jun 01

Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M. 2004. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. Mar; 37: 914-39

Krieger, C, Zhang, P, Mueller, LA, Wang, A., Paley, S., Arnaud, M., Pick. J. Rhee, S. and Karp, P. 2004. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2004 Jan 1; 32: (Database issue):D438-42.

Mueller, L.A., Zhang, P., Rhee, S. 2003. AraCyc: An Arabidopsis thaliana biochemical pathway database. Plant Physiol 132: 453-460

Meinke DW, Meinke LK, Showalter TC, Schissel AM, Mueller LA, nd Tzafrir I. 2003. A sequence based map of Arabidopsis genes with mutant phenotypes. Plant Physiology 131: 409-418

Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J,, Zhang P. 2003. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 2003 Jan 1; 31: 224-8. PMID: 12519987

Garcia-Hernandez M, Berardini TZ, Chen G, Crist D, Doyle A, Huala E, Knee E, Lambrecht M, Miller N, Mueller LA, Mundodi S, Reiser L, Rhee SY, Scholl R, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P. 2002. TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics. Nov; 2: 239-53

Mitra M., Shah N., Mueller, L., Pin S. and Fedoroff N. 2002. StressDB: A locally installable web-based relational microarray database designed for small user communities. Comparative and Functional Genomics. v 3: (#2) pp 91-96

Tobler AR, Liu N, Mueller L, Shooter EM. 2002. Differential aggregation of the Trembler and Trembler J mutants of peripheral myelin protein 22. Proc Natl Acad Sci U S A; 99: 483-8. PMID: 11752407

Reiser, L., Mueller, L.A., Rhee, S. 2001. Surviving in a sea of data: a survey of plant genome data resource and issues in building data management systems. Plant Molecular Biology 48: p59-74

Mueller, L.A., Walbot, V. 2001. Models for the Vacuolar Sequestration of Anthocyanins. Romeo, J.T, Saunders, J.A., Matthews, B.F, Editors. Recent Advances in Phytochemistry, Volume 35: 297-312

Huala, E; Dickerman, A; Garcia-Hernandez, M; Weems, D; Reiser, L; LaFond, F; Hanley, D; Kiphart, D; Zhuang, J; Huang, W; Mueller, L. A.; Bhattacharyya, D; Bhaya, D; Sobral, B; Beavis, B, Somerville, C; and Rhee, SY. 2001. The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. Jan 1; 29: 102-5

Mueller, L.A., Silady, R., Goodman, C.D., Walbot, V. 2000. AN9, a glutathione S-transferase from Petunia required for vacuolar sequestration of anthocyanins, is a flavonoid binding protein. Plant Physiology 123: 1561-1570

Mueller, L. A., Hinz, U., Uze, M., Sautter, C., Zryd, J. P. 1997. Biochemical Complementation of the betalain biosynthetic pathway in Portulaca grandiflora by a fungal 3,4-dihydroxyphenylalanine dioxygenase. Planta 203: 260-263

Mueller, L.A., Hinz, U., Zryd, J.P. 1996. Recombinant DOPA dioxygenase catalyzes the conversion of DOPA to muscaflavin and betalamic acid. Phytochemistry 44: 567-569

Mueller, L.A., Hinz, U., Zryd, J.P. 1996. Characterization of a tyrosinase from Amanita muscaria involved in betalain biosynthesis. Phytochemistry 42: 1511-1515

Features

Features

How will researchers store and retrieve scientific information in the future?

feature released -2008

How will researchers store and retrieve scientific information in the future?Consider that thousands of scientists are working worldwide to identify all the genes in a wide variety of plants. Then, consider that a plant like tomato has about 35,000 genes, some of which function in complex networks. And then consider that new genetic discoveries are being made each and every day about how these genes are regulated and how they interact. How can all this information be efficiently stored, updated and made accessible to scientists in a timely manner so they can use it and build on it?

This is the question that Lukas Mueller’s laboratory at BTI is answering. Among other projects, Mueller’s group coordinates the Solanaceae Genomics Network — a database of all the genetic information known about solanaceous plants, such as tomatoes and peppers. He’s also involved in the tomato genome sequencing project, which is the work of scientists in 10 countries.

Mueller is developing software that will make it easier for scientists to access vast amounts of genomic data. He’s also working to make it simpler for scientists to annotate, or update, the data as they make new discoveries. It’s similar to the idea that gave rise to Wikipedia — an encyclopedia that can be added to or revised by anyone who reads it. The difference is that Mueller’s software and the database it runs are specifically designed for complex biological data.

Until the advent of the Internet, scientists could only share the results of their research with others through personal communications and by publishing their work in scientific journals. But neither communication method enabled colleagues to access all the data that backed up the results. With the software Mueller is developing, scientists not only can see the results of others’ work, they can also see — and use — the data the results were derived from.

Mueller’s goal is to make these databases so easy to use that they will become the primary place for storing, sharing, updating and accessing genomics information. At that point, the practical applications of his work would multiply. For instance, plant breeders could use the database to more quickly develop new varieties of crop plants with innovative genetic characteristics, such as higher yield or enhanced nutritional quality.

Lab Members

Lab Members

Jeremy Edwards
Jeremy Edwards
Research Associate
Office/Lab: 217
jde22@cornell.edu
Office: 607 254 3569
Lab:
Noe Fernandez
Noe Fernandez
Postdoc
Office/Lab: 207
nf232@cornell.edu
Office: 607 254 5480
Lab:
Thomas Fisher-York
Thomas Fisher-York
Bioinformatics Analyst
Office/Lab: 217
tly2@cornell.edu
Office: 607 254 3569
Lab:
Hartmut Foerster
Hartmut Foerster
Research Associate
Office/Lab: 207
hf263@cornell.edu
Office: 607 254 5480
Lab:
Naama Menda
Naama Menda
Postdoc
Office/Lab: 217
nm249@cornell.edu
Office: 607 254 3569
Lab:
Susan Strickler
Susan Strickler
Postdoc
Office/Lab: 217
srs57@cornell.edu
Office: 607 254 3569
Lab:
Isaak Yosief Tecle
Isaak Yosief Tecle
Research Associate
Office/Lab: 217
iyt2@cornell.edu
Office: 607 254 3569
Lab:
Aimit Yan
Aimit Yan
Research Associate
Office/Lab: 207
ay247@cornell.edu
Office: 607 254 5480
Lab:

PGRP

Plant Genome Research Program

Research ProjectSGN bioinformatics and genomics

Participating Interns

2012 – Interns
2011 – Interns
2008 – Interns