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Lukas Mueller
 &emdash;  Faculty

Lukas Mueller
Office/Lab: 221
Affiliations:
  • Section of Plant Breeding and Genetics
  • School of Integrative Plant Science
  • Cornell University
Graduate Fields: Plant Breeding
Research Areas:

Research Overview

In recent years, technological advances in fields such as sequencing have transformed certain aspects of biology into an information-based discipline.

To make this abundance of data—often called Big Data—useful to researchers and breeders, it needs to be organized and made accessible. Towards this goal, the Mueller lab designs and implements databases that assist scientists in their research and plant breeders in more efficient crop improvement.

Our databases and software make transcriptomic, genotypic and phenotypic data from thousands of experiments accessible to the public, often focusing on under-researched staple crops from food-insecure regions. A method called Genomic Selection that uses high-throughput genotyping technologies, such as genotyping-by-sequencing (GBS), and large phenotyping data sets allows for rapid prediction of desirable traits in new plant crosses.

Based on these tools, the Mueller laboratory collaborates on a variety of different projects. With the Nextgen Cassava project, we have created Cassavabase, a database specifically designed for cassava breeders in Africa. We coordinate the Solanaceae Genomics Network—a compilation of all the genetic information known about solanaceous plants, such as tomato, petunia and Nicotiana. We are also developing breeding databases for yam, sweet potato and the cooking banana and we work with the Genomic and Open-source Breeding Informatics Initiative (GOBII) to streamline crop breeding for five staple crops—wheat, rice, maize, sorghum and chickpea. Finally, the Mueller group is involved in multiple genome sequencing projects, including tomato, coffee, petunia and Nicotania benthamiana.

Links:
Sol Genomics Network
Cassavabase
Yambase
Sweetpotatobase
Musabase
Rtbbase

Publications

  • An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita 2015

    Wyatt, L.E., Strickler, S.R., Mueller, L.A., and Mazourek, M.
    Horticulture Research , 14070,  14070
    Full text...
  • Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta) 2015

    Perrois, C., Strickler, S.R., Mathieu, G., Lepelley, M., Bedon, L., Michaux, S., Husson, J., Mueller, L., and Privat, I.
    Planta 241(1),  179-191
    Full text...
  • The Sol Genomics Network (SGN)—from genotype to phenotype to breeding 2014

    Fernandez-Pozo, N., Menda, N., Edwards, J.D., Saha, S., Tecle, I.Y., Strickler, S.R., Bombarely, A., Fisher-York, T., Pujar, A., Foerster, H., Yan, A., and Mueller, L.A.
    Nucl. Acids Res. 43 (D1),  D1036-D1041
    Full text...
  • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases 2014

    Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C.A., Holland, T.A., Keseler, I.M., Kothari, A., Kubo, A., Krummenacker, M., Latendresse, M., Mueller, L.A., Ong, Q., Paley, S., Subhraveti, P., Weaver, D.S., Weerasinghe, D., Zhang, P.F., and Karp, P.D.
    Nucleic Acids Research 42,  D459-D471.
    Full text...
  • The SGN VIGS tool: user-friendly software to design virus-induced gene silencing (VIGS) constructs for functional genomics 2015

    Fernandez-Pozo, N., Rosli, H.G., Martin, G.B., and Mueller, L.A.
    Mol. Plant 3,  486-488
    Full text...
  • Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives 2014

    Strickler, S.R., Bombarely, A., Munkvold, J.D., Menda, N., Martin, G.B., and Mueller, L.A.
    PeerJ PrePrints 2,  e377v1
    Full text...
  • A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. 2012

    Bombarely, A., Rosli, H.G., Vrebalov, J., Moffett, P., Mueller, L.A., and Martin, G.B.
    Mol. Plant-Microbe Interact. 25,  1523-1530
    Full text...
  • Linking the potato genome to the conserved ortholog set (COS) markers 2013

    Lindqvist-Kreuze, H., Cho, K., Portal, L., Rodriguez, F., Simon, R., Mueller, L.A., Spooner, D.M., and Bonierbale, M.
    BMC Genetics 14,  51
    Full text...
  • Advances in tomato research in the post-genome era 2013

    Menda, N., Strickler, S.R., and Mueller, L.A.
    Plant Biotechnology 30,  243-256
    Full text...
  • From manual curation to visualization of gene families and networks across Solanaceae plant species 2013

    Pujar, A., Menda, N., Bombarely, A., Edwards, J.D., Strickler, S.R., and Mueller, L.A.
    Database : The Journal of Biological Databases and Curation (Oxford) 2013,  bat028
    Full text...
  • The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions 2012

    Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, L., 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., Wang, J., Li, Y., Fei, Z., and Xu, Y.
    Nature Genetics 45,  51-58
    Full text...
  • Molecular Phylogeny of Daucus (Apiaceae) 2013

    Spooner, D., Rojas, P., Bonierbale, M., Mueller, L.A., Srivastav, M., Senalik, D., and Simon, P.
    Systematic Botany 38,  850-857
    Full text...
  • The tomato kinome and the TOKN ORFeome: resources for the study of kinases and signal transduction in tomato and Solanaceae. 2014

    Singh, D.K., Calviño, M., Brauer, E.K.*, Fernandez-Pozo, N.*, Strickler, S., Yalamanchili, R., Suzuki, H., Aoki, K., Shibata, D., Stratmann, J.W., Popescu, G.V., Mueller, L., and Popescu, S.C. *co-third authors
    Mol. Plant Microbe Interact. 27,  7-17. Article featured as an MPMI Editor’s Pick: Kinases and Signal Transduction in Tomato and Solanaceae Species, 16 January 2014. REU students Ann Guggisberg and Jade Newsome are acknowledged for their contributions
    Full text...
  • Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective 2012

    Bombarely, A., Edwards, K.D., Sanchez-Tamburrino, J., and Mueller, L.A.
    BMC Genomics 13,  406
    Full text...
  • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases 2012

    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.
    Nucleic Acids Research 40,  D742-D753
    Full text...
  • Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota) 2012

    Cai, D.Y., Rodriguez, F., Teng, Y.W., Ane, C., Bonierbale, M., Mueller, L.A., and Spooner, D.M.
    BMC Evol. Biol. 12,  70
    Full text...
  • Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case 2012

    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.
    Proteomics, 12,  761-774
    Full text...
  • Trait diversity and potential for selection indices based on variation among regionally adapted processing tomato germplasm 2012

    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.
    J. Am. Soc. Hortic. Sci. 137,  427-437
    Full text...
  • Designing a transcriptome next-generation sequencing project for a nonmodel plant species 2012

    Strickler, S.R., Bombarely, A., and Mueller, L.A.
    Am. J. Bot. 99,  257-266
    Full text...
  • The Tomato Genome Consortium. 2009. A snapshot of the emerging tomato genome sequence. 2009

    The Plant Genome 2,  78-92
    Full text...
  • The ‘PUCE CAFE’ project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits 2011

    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.
    BMC Genomics 12,  5
    Full text...
  • The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data 2011

    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.
    Database: The Journal of Biological Databases and Curation ]2011],  bar051
    Full text...
  • The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl 2011

    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.
    Nucleic Acids Res. 39,  D1149-1155
    Full text...
  • TobEA: an atlas of tobacco gene expression from seed to senescence 2010

    Edwards, K.D., Bombarely, A., Story, G.W., Allen, F., Mueller, L.A., Coates, S.A., and Jones, L.
    BMC Genomics 11,  142
    Full text...
  • Advances in Coffea genomics 2010

    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.
    Advances in Botanical Research 53,  23-63
    Full text...
  • Analysis of Ultra Low Genome Conservation in Clostridium difficile 2010

    Scaria, J., Ponnala, L., Janvilisri, T., Yan, W.W., Mueller, L.A., and Chang, Y.F.
    PLoS ONE 5,  e15147
    Full text...
  • solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database 2010

    Tecle, I.Y., Menda, N., Buels, R.M., van der Knaap, E., and Mueller, L.A.
    BMC Bioinformatics 11,  525
    Full text...
  • Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants 2010

    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.
    Plant Physiology 153,  1479-1491
    Full text...
  • A dynamic interface for capsaicinoid systems biology 2009

    Mazourek, M., Pujar, A., Borovsky, Y., Paran, I., Mueller, L., and Jahn, M.M.
    Plant Physiology 150,  1806-1821
    Full text...
  • A community-based annotation framework for linking Solanaceae genomes with phenomes 2008

    Menda, N., Buels, R.M., Tecle, I., and Mueller, L.A.
    Plant Physiology 147,  1788-1799
    Full text...
  • 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 2006

    Wu, F., Mueller, L.A., Crouzillat, D., Petiard, V., and Tanksley, S.D.
    Genetics 174,  1407-1420
    Full text...
  • EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot 2006

    Carlson, J.E., Leebens-Mack, J.H., Wall, P.K., Zahn, L.M., Mueller, L.A., Landherr, L.L., Hu, Y., Ilut, D.C., Arrington, J.M., Choirean, S., Becker, A., Field, D., Tanksley, S.D., Ma, H., and dePamphilis, C.W.
    Plant Mol. Biol. 62,  351-369
    Full text...
  • Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts 2005

    Lin, C., Mueller, L.A., Carthy, J.M., Crouzillat, D., Petiard, V., and Tanksley, S.D.
    Theor. Appl. Genet. 112(1),  114–130
    Full text...
  • MetaCyc and AraCyc. Metabolic pathway databases for plant research 2005

    Zhang, P., Foerster, H., Tissier, C.P., Mueller, L., Paley, S., Karp, P.D., and Rhee, S.Y.
    Plant Physiology 138,  27-37
    Full text...
  • The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL) 2005

    Mueller, L. A., Tanksley, S.D., Giovannoni, J., Van Eck, J., Stack, S., Choi, D., Kim, B.D., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Seymour, G., Bishop, G., Bryan, G., Sharma, R., Khurana, J., Tyagi, A., Chattopadhyay, D., Singh, N.K., Stiekema, W., Lindhout, P., Jesse, T., Lankhorst, R.K., Bouzayen, M., Shibata, D., Tabata, S., Granell, A., Botella, M.A., Giuliano, G., Frusciante, L., Causse, M., and Zamir, D.
    Comparative and Functional Genomics 6,  153-158
    Full text...
  • Querying and computing with BioCyc databases 2005

    Krummenacker, M., Paley, S.M., Mueller, L.A., Yan, T., and Karp, P.D.
    Bioinformatics 21,  3454-3455
    Full text...
  • Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments 2005

    Wang, Y., van der Hoeven, R.S., Nielsen, R., Mueller, L.A., and Tanksley, S.D.
    Theor. Appl. Genet. 6,  1-13
    Full text...
  • PatMatch: a program for finding patterns in peptide and nucleotide sequences 2005

    Yan, T., Yoo, D., Berardini, T.Z., Mueller, L.A., Weems, D.C., Weng, S., Cherry, J.M., Rhee, S.Y.
    Nucleic Acids Res. 33 (Web Server issue),  W262-266
    Full text...
  • Floral gene resources from basal angiosperms for comparative genomics research 2005

    Albert, V.A., Soltis, D.E., Carlson, J.E., Farmerie, W.G., Wall, P.K., Ilut, D.C., Solow, T.M., Mueller, L.A., Landherr, L.L., Hu, Y., Buzgo, M., Kim, S., Yoo, M.J., Frohlich, M.W., Perl-Treves, R., Schlarbaum, S.E., Bliss, B.J., Zhang, X., Tanksley, S.D., Oppenheimer, D.G., Soltis, P.S., Ma, H., DePamphilis, C.W., and Leebens-Mack, J.H.
    BMC Plant Biol. 5,  5
    Full text...
  • The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond 2005

    Mueller, L.A., Solow, T.H., Taylor, N., Skwarecki, B., Buels, R., Binns, J., Lin, C., Wright, M.H., Ahrens, R., Wang, Y., Herbst, E.V., Keyder, E.R., Menda, N., Zamir, D., and Tanksley, S.D.
    Plant Physiology 138,  1310-1317
    Full text...
  • Related Articles, Links Abstract Functional annotation of the Arabidopsis genome using controlled vocabularies 2004

    Berardini, T.Z., Mundodi, S., Reiser, L., Huala, E., Garcia-Hernandez, M., Zhang, P., Mueller, L.A., Yoon, J., Doyle, A., Lander, G., Moseyko, N., Yoo, D., Xu, I., Zoeckler, B., Montoya, M., Miller, N., Weems, D., and Rhee, S.Y.
    Plant Physiology 135,  745-55
    Full text...
  • MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes 2004

    Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L.A., Rhee, S.Y., and Stitt, M.
    Plant J. 37,  914-939
    Full text...
  • MetaCyc: a multiorganism database of metabolic pathways and enzymes 2004

    Krieger, C., Zhang, P., Mueller, L.A., Wang, A., Paley, S., Arnaud, M., Pick, J., Rhee, S., and Karp, P.
    Nucleic Acids Research 32, Database Issue,  438-442
    Full text...
  • AraCyc: An Arabidopsis thaliana biochemical pathway database 2003

    Mueller, L.A., Zhang, P., and Rhee, S.
    Plant Physiology 132,  453-460
    Full text...
  • A sequence based map of Arabidopsis genes with mutant phenotypes 2003

    Meinke, D.W., Meinke, L.K., Showalter, T.C., Schissel, A.M., Mueller, L.A., and Tzafrir, I.
    Plant Physiology 131,  409-418
    Full text...
  • The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community 2003

    Rhee, S.Y., Beavis, W., Berardini, T.Z., Chen, G., Dixon, D., Doyle, A., Garcia-Hernandez, M., Huala, E., Lander, G., Montoya, M., Miller, N., Mueller, L.A., Mundodi, S., Reiser, L., Tacklind, J., Weems, D.C., Wu, Y., Xu, I., Yoo, D., Yoon, J., and Zhang, P.
    Nucleic Acids Research 31,  224-228
    Full text...
  • TAIR: a resource for integrated Arabidopsis data 2002

    Garcia-Hernandez, M., Berardini, T.Z., Chen, G., Crist, D., Doyle, A., Huala, E., Knee, E., Lambrecht, M., Miller, N., Mueller, L.A., Mundodi, S., Reiser, L., Rhee, S.Y., Scholl, R., Tacklind, J., Weems, D.C., Wu, Y., Xu, I., Yoo, D., Yoon, J., and Zhang, P.
    Funct. Integr. Genomic. 2,  239-253
    Full text...
  • StressDB: A locally installable web-based relational microarray database designed for small user communities 2002

    Mitra, M., Shah, N., Mueller, L., Pin, S., and Fedoroff, N.
    Comp. Funct. Genom. 3,  91–96.
    Full text...
  • Differential aggregation of the Trembler and Trembler J mutants of peripheral myelin protein 22 2002

    Tobler, A.R., Liu, N., Mueller, L., and Shooter, E.M.
    P. Natl. Acad. Sci. U S A 99,  483-488
    Full text...
  • Surviving in a sea of data: a survey of plant genome data resource and issues in building data management systems 2001

    Reiser, L., Mueller, L.A., Rhee, S.
    Plant Molecular Biology 48,  59-74
    Full text...
  • Models for the Vacuolar Sequestration of Anthocyanins 2001

    Mueller, L.A., Walbot, V.
    In Recent Advances in Phytochemistry. (Romeo, J.T, Saunders, J.A., Matthews, B.F, Editors.) 35,  297-312
    Full text...
  • The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant 2001

    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, S.Y.
    Nucleic Acids Research 29,  102-105
    Full text...
  • AN9, a glutathione S-transferase from Petunia required for vacuolar sequestration of anthocyanins, is a flavonoid binding protein 2000

    Mueller, L.A., Silady, R., Goodman, C.D., and Walbot, V.
    , 123, 1561-1570 123,  1561-1570
    Full text...
  • Biochemical Complementation of the betalain biosynthetic pathway in Portulaca grandiflora by a fungal 3,4-dihydroxyphenylalanine dioxygenase 1997

    Mueller, L. A., Hinz, U., Uze, M., Sautter, C., Zryd, J.P.
    Planta 203,  260-263
    Full text...
  • Recombinant DOPA dioxygenase catalyzes the conversion of DOPA to muscaflavin and betalamic acid 1996

    Mueller, L.A., Hinz, U., Zryd, J.P.
    Phytochemistry 44,  567-569
    Full text...
  • Characterization of a tyrosinase from Amanita muscaria involved in betalain biosynthesis 1996

    Mueller, L.A., Hinz, U., Zryd, J.P.
    Phytochemistry 42,  1511-1515
    Full text...

Intern Projects

Interns in the Mueller lab work on a variety of bioinformatics and genomics projects and gain experience in the following areas: genome assembly, structural and functional annotation, biochemical pathways, comparative genomics, ontology development and data presentation and visualization.

Interns

Research Utilization

Plant Bioinformatics

Bioinformatics tools and databases are a cornerstone of modern plant research. The Mueller lab is developing resources such as the SOL Genomics Network (SGN, http://solgenomics.net) and Cassavabase (http://cassavabase.org/), which help researchers navigate and exploit vast amounts of information. These websites contain genomic, genetic, and phenotypic data and provide easy-to-use tools for researchers to query, analyze and visualize the data.

SGN is database for the Solanaceae family, which includes such agronomically important crops as tomato, potato and peppers. The database is centered around the tomato reference sequence generated by the International Tomato Genome Sequencing Project released in 2012. SGN stores genomic and breeding data, including genetic and physical maps with markers, QTLs, gene sequences, functional genomics data, including expression and pathway data, and phenotypic data. The database also supports community curation, which enables users to contribute annotation and other data, such as images, to locus and stock pages.

Cassavabase is the database for the Nextgen Cassava project (http://nexgencassava.org/), which has the goal of improving Cassava breeding by applying high throughput genotyping technologies, and using genomic selection to accelerate the breeding cycle. The database contains genotypic data for lines in the breeding program, as well as extensive phenotypic data for training populations, the tools to correlate genotypes with phenotypes and to predict breeding values from genotypic information.

All code developed in the Mueller lab is open-source and freely available.

The website code created for SGN and Cassavabase represents a generic, reusable, modular and flexible platform, suitable for use by other organism databases. The long-term goal is to provide opportunities for academic and private organizations to cooperate more closely on software development, reducing the re-implementation of the same site features by different databases. Not only would adoption of a common platform reduce the syndrome of re-inventing the wheel, but it would also benefit users, and would greatly facilitate the integration of public data into proprietary databases. The Mueller lab also welcomes collaborations involving the assembly, annotation, and analysis of next generation genome and transcriptome data for a wide variety of plants.

Collaboration and Consulting Opportunities

Custom bioinformatics tools and databases

Collaborations and Consulting

In the News

Enabling Technologies

  • Nicotiana benthamiana

    Bioinformatics Tools BLAST tool VIGS Tool CRISPR-P Tool CCTop CRISPR tool Genome sequence Gene annotation Metabolic Pathways Proteomics Databases Genome Browser VIGS: genes to phenotypes database Nb Experimental Protocols and Resources Virus-induced gene silencing – 1 (requires JoVE subscription) PTI assay (requires JoVE subscription) First papers to use Read more »