Lukas Mueller

Assistant Scientist

Office/Lab: Room 221

Contact: lam87@cornell.edu / (607) 255-6557 Fax (607) 254-1242

Interests

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.

Publications

View Publications

Menda N, Buels RM, Tecle I, Mueller LA. 2008. A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol 147(4): 1788-99
Datema E, Mueller LA, Buels R, Giovannoni JJ, Visser RG, Stiekema WJ, van Ham RC. 2008. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. BMC Plant Biol. 2008 Apr 8: 34. PMID: 18405374
Mueller LA, Mills AA, Skwarecki B, Buels RM, Menda N, Tanksley SD. 2008. The SGN comparative map viewer. Bioinformatics. 2008 Feb 1 24(3): 422-3
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(3): 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(3): 351-69
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
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 : 1-17 [PMID: 16273343]
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(1): 5
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(1): 27-37
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
Markus Krummenacker, Suzanne M. Paley, Lukas A. Mueller, Thomas Yan, Peter D. Karp. 2005. Querying and computing with BioCyc databases. Bioinformatics 21(16): 3454-3455
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(3): 1310-7
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
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(6): 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.
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(2): 745-55. Epub 2004 Jun 01
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
Mueller, L.A., Zhang, P., Rhee, S. 2003. AraCyc: An Arabidopsis thaliana biochemical pathway database. Plant Physiol 132: 453-460
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(1): 224-8. PMID: 12519987
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(1): 483-8. PMID: 11752407
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
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(6): 239-53
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
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
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(1): 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. Characterization of a tyrosinase from Amanita muscaria involved in betalain biosynthesis. Phytochemistry 42: 1511-1515
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