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:

Citrus Greening Solutions
A systems-based pipeline approach for delivering commercial, grove-deployable solutions using a novel therapeutic delivery strategy and citrus transgenics.

Cassavabase
Access to data and tools for breeders and researchers, including genomic selection algorithms and analysis capacity, a cassava genome browser, cassava ontology tools, phenotyping tools, and social networking.

Musabase
A breeding database designed for advanced breeding methods in banana breeding.

Rtbbase
A collection of Root Tubers & Banana Databases, which hold genomic and phenotypic information for next generation breeding applications.

Sol Genomics Network
A site for genome data of Solanaceae species such as tomato, potato, and pepper, and related to the tomato genome sequencing project.

Sweetpotatobase
Part of the Genomics Tools for Sweet Potato (GT4SP) Improvement Project focused on developing a set of “next generation” breeder tools for African sweetpotato breeders in Africa.

Yambase
A database about breeding data for Yam (genus Dioscorea). Yam species that are being used for breeding include , Dioscorea rotundata, Dioscorea cayenensis (both are native to Africa and the major cultivated species), Dioscorea aleata (native to Southeast Asia), and Dioscorea praehensilis, as well as several other species.

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
High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening
2018.
Shinozaki, Y., Nicolas, P., Fernandez-Pozo, N., Ma, Q., Evanich, D. J., Shi, Y., Xu, Y., Zheng, Y., …
Nature Communications.
9
:
The Tomato Expression Atlas
2017.
Fernandez-Pozo, N., Zheng, Y., Snyder, S. I., Nicolas, P., Shinozaki, Y., Fei, Zhangjun, Catala, Car…
Bioinformatics (Oxford, England).
33
:
2397–2398
Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell
2017.
Villarino, G. H., Scanlon, Michael J., Scanlon, Michael J., Mueller, Lukas A., Bombarely, A., Mattso…
Genes (Basel).
8
:
195–195
Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica
2017.
Carlson, K. D., Fernandez-Pozo, N., Bombarely, A., Pisupati, R., Mueller, Lukas A., Madlung, A.
BMC Genomics.
18
:
A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency
2017.
Edwards, K. D., Fernandez-Pozo, N., Drake-Stowe, K., Humphry, M., Evans, A. D., Bombarely, A., Allen…
BMC Genomics.
18
:
Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut
2017.
Kruse, A., Fattah-Hosseini, S., Saha, S., Johnson, R., Warwick, E. R., Sturgeon, K., Mueller, Lukas …
PLOS One.
12
:
e0179531–e0179531
Rapid defense responses in maize leaves induced by Spodoptera exigua caterpillar feeding
2017.
Tzin, V., Hojo, Y., Strickler, S. R., Bartsch, L. J., Archer, C. M., Ahern, K. R., Zhou, S., Christe…
Journal of Experimental Botany.
68
:
4709–4723
BioCyc: Online Resource for Genome and Metabolic Pathway Analysis
2016.
Caspi, R., Billington, R., Foerster, H., Fulcher, C. A., Keseler, I., Kothari, A., Krummenacker, M.,…
FASEB JOURNAL.
30
:
Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
2016.
Bombarely, A., Moser, M., Amrad, A., Bao, M., Bapaume, L., Barry, C. S., Bliek, M., Boersma, M. R., …
Nature Plants.
2
:
16074–16074
Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data
2016.
Edwards, J. D., Baldo, A. M., Mueller, Lukas A.
Database : the journal of biological databases and curation.
2016
:
baw107–baw107
Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L)
2016.
Osorio-Guarín, J. A., Enciso-Rodríguez, F. E., González, C., Fernández-Pozo, N., Mueller, Lukas …
BMC Genomics.
17
:
Genes conserved for arbuscular mycorrhizal symbiosis identified through phylogenomics
2016.
Bravo, A., York, T., Pumplin, N., Mueller, Lukas A., Harrison, Maria J.
Nature Plants.
2
:
15208–15208
Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae
2016.
Gates, D. J., Strickler, S. R., Mueller, Lukas A., Olson, B. JSC, Smith, S. D.
Journal of Molecular Evolution.
83
:
26–37
Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin
2016.
Wyatt, L. E., Strickler, S. R., Mueller, Lukas A., Mazourek, M.
Horticulture Research.
3
:
16045–16045
Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening
2016.
Jouffroy, O., Saha, S., Mueller, Lukas A., Quesneville, H., Maumus, F.
BMC Genomics.
17
:
Dynamic Maize Responses to Aphid Feeding Are Revealed by a Time Series of Transcriptomic and Metabolomic Assays
2015.
Tzin, V., Fernandez-Pozo, N., Richter, A., Schmelz, E. A., Schoettner, M., Schäfer, M., Ahern, K. R…
Plant Physiology.
169
:
1727–1743
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, Gregory B., Mueller, Lukas A.
Molecular Plant.
8
:
486–488
Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives
2015.
Strickler, S. R., Bombarely, A., Munkvold, J. D., York, T., Menda, N., Martin, Gregory B., Mueller, …
PeerJ.
2015
:
e793–e793
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, Lukas A., Mazourek, Michael
Horticulture Research.
2
:
14070–14070
The Sol Genomics Network (SGN)–from genotype to phenotype to breeding
2015.
Fernandez-Pozo, N., Menda, N., Edwards, J. D., Saha, S., Tecle, I. Y., Strickler, S. R., Bombarely, …
Nucleic Acids Research.
43
:
D1036–D1041

Contact:

Boyce Thompson Institute
533 Tower Rd.
Ithaca, NY 14853
607.254.1234
contact@btiscience.org