Lukas Mueller

Associate Professor
Lukas Mueller
lam87@cornell.edu
Office/Lab: 221
Phone: 607-255-6557
Office/Lab: 221
Email: lam87@cornell.edu
Office Phone: 607-255-6557
Affiliations: Section of Plant Breeding and Genetics / School of Integrative Plant Science / Cornell University
Graduate Fields: Plant Breeding
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

  • BTI’s Mueller Lab and visiting researchers collaborate to improve important crop databases

    During June and July at BTI, visiting scholars from crop breeding programs in Nigeria, Nairobi, and Uganda have been working closely with researchers in Lukas Mueller’s group to discuss ways to improve the development of online resources related to two of Africa’s most important staple crops: cassava and banana. Read more »
  • Global partnerships for improving cassava

    Cassava geneticist Ismail Yusuf Rabbi from the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria visited BTI and Cornell University last week to discuss his ongoing collaboration with NextGen Cassava. Read more »
  • BTI researchers share latest research at ag-genomics conference

    The offices of data scientists at BTI emptied out earlier this month as a contingent of researchers flew to San Diego for the 25th annual Plant and Animal Genome Conference. Genomic researchers from around the world gathered at the meeting to network, consult with colleagues and hear the newest advances in genome sequencing technology and […] Read more »
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.

Internship Program | Projects & FacultyApply for an Internship
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.
Molecular Plant.
3,
486-488
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
Advances in tomato research in the post-genome era
2013.
Menda, N., Strickler, S.R., and Mueller, L.A.
Plant Biotechnology.
30,
243-256
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
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 td>.
]2011],
bar051
View
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
View
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
View
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
View
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
View
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
View
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
View
Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato
2008.
Datema, E., Mueller, L.A., Buels, R., Giovannoni, J.J., Visser, R.G.F., Stiekema, W.J., and van Ham, R.C.H.J.
BMC Plant Biol..
8,
34
View
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
View
Tomato
2007.
Labate, A., Grandillo, S., Fulton, T., Muños, S., Caicedo, A.L., Peralta, I., Ji, Y., Chetelat, R.T., Scott, J.W., Gonzalo, M.J., Francis, D., Yang, W., van der Knaap, E., Baldo, A.M., Smith-White, B., Mueller, L.A., Prince, J.P., Blanchard, N.E., Storey, D.B., Stevens, M.R., Robbins, M.D., Wang, J.-F., Liedl, B.E., O’Connell, M.A., Stommel, J.R., Aoki, K., Iijima, Y., Slade, A.J., Hurst, S.R., Loeffler, D., Steine, M.N., Vafeados, D., McGuire, C., Freeman, C., Amen, A., Goodstal, J., Facciotti, D., VanEck, J., and Causs, M.
Genome Mapping and Molecular Breeding in Plants.
5,Vegetables. (C Kole ed.), Springer-Verlag, Berlin Heidelberg New York,
pp 1: 131
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
AraCyc: An Arabidopsis thaliana biochemical pathway database
2003.
Mueller, L.A., Zhang, P., and Rhee, S.
Plant Physiology.
132,
453-460
View
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
View
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
View
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
View
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
View
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
View
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
View
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
View
Characterization of a tyrosinase from Amanita muscaria involved in betalain biosynthesis
1996.
Mueller, L.A., Hinz, U., Zryd, J.P.
Phytochemistry.
42,
1511-1515
View