Lukas Mueller

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: Adjunct Professor / 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:

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.

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

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

Development on Citrus medica infected with ‘Candidatus Liberibacter asiaticus’ has sex-specific and -nonspecific impacts on adult Diaphorina citri and its endosymbionts
2020.
Coates, L.C., Mahoney, J., Ramsey, J.S., Warwick, E., Johnson, R., MacCoss, M.J., Krasnoff, S.B., Ho…
PloS One.
15
:
Reinterpretation of ‘sperm pump’ or ‘sperm syringe’ function with notes on other male internal reproductive organs in the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae)
2020.
Cicero, J.M., Hunter, W.B., Cano, L.M., Saha, S., Mueller, Lukas A., Brown, S.J.
Arthropod Struct Dev..
54
:
Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum)
2020.
Ziaid, S.S., Naqvi, R.Z., Asif, M., Strickler, Susan, Shakir, S., Shafiq, M., Khan, A.M., Amin, I., …
Plant Biotechnol J..
18
:
691–706
Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages
2020.
Baba, V.Y., Powell, A.F., Ivamoto-Suzuki, S.T., Pereira, L.F.P., Vanzela, A.L.L., Giacomin, R.M., St…
Sci Rep..
10
:
12048
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook
2020.
Foerster, H., Battey, J.N.D., Sierro, N., Ivanov, N.V., Mueller, Lukas A.
Brief Bioinform..
:
BrAPI-an Application Programming Interface for Plant Breeding Applications
2020.
Selby, P., Abeeloos, R., Backlund, J.E., Salida, M.B., Bauchet, G., Benites-Alfaro, O.E., Birkett, C…
Bioinformatics..
:
Exploiting the diversity of tomato: the development of a phenotypically and genetically detailed germplasm collection.
2020.
Mata-Nicolas, E., Montero-Pau, J., Gimeno-Paez, E., Garcia-Carpintero, V., Ziarsolo, P., Menda, N., …
Hortic Res..
:
Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by ‘Candidatus Liberibacter asiaticus‘.
2020.
Ramsey, J.S., Chin, E.L., Chavez, J.D., Saha, S., Mischuk, D., Mahoney, J., Mohr, J., Robison, F.M.,…
J Proteome Res.
:
Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)
2020.
Züst, T, Strickler, S.R., Powell, A.F., Mabry, M.E., An, H., Mirzaei, M., York, T., Holland, C.K., …
Elife.
9
:
e51712
Longitudinal transcriptomic, proteomic, and metabolomic analyses of Citrus sinensis (L.) Osbeck graft-inoculated with ‘Candidatus Liberibacter asiaticus’.
2019.
Chin, E.L., Ramsey, J.S., Mishchuk, D.O., Saha, S., Foster, E., Chavez, J.D., Howe, K., Zhong, X., P…
J Proteome Res..
:
Transcriptomic analysis of cultivated cotton Gossypium hirsutum provides insights into host responses upon whitefly-mediated transmission of cotton leaf curl disease
2019.
Naqvi R.Z., Zaidi S.S., Mukhtar M.S., Amin I., Mishra B., Strickler, S., Mueller, Lukas A., Asif, M.…
PLOS One.
:
BrAPI—an application programming interface for plant breeding applications
2019.
Selby, P. Abbeloos, R., Backlund, J.E., Basterrechea S., Martin, Bauchet, G., Benites-Alfaro, O.E., …
Bioinformatics.
:
Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection
2018.
Gonda, I., Ashrafi, H., Lyon, D.A., Strickler, S.R., Hulse-Kemp, A.M., Ma, Q., Sun, H., Stoffel, K.,…
The Plant Genome.
12
:
Molecular Markers to Select for the j-2-mediated Jointless Pedicel in Tomato
2018.
Lee, T. G., Shekasteband, R., Menda, N., Mueller, Lukas A., Hutton, S. F.
HortScience.
53
:
153–158
Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions
2018.
Nunes, R. DC, Orozco-Arias, S., Crouzillat, D., Mueller, Lukas A., Strickler, S. R., Descombes, P., …
Frontiers in Plant Science.
9
:
Linkage between the I-3 gene for resistance to Fusarium wilt race 3 and increased sensitivity to bacterial spot in tomato
2018.
Li, J., Chitwood, J., Menda, N., Mueller, Lukas A., Hutton, S. F.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.
131
:
145–155
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
:
Impact of intravenous thrombolysis on recanalization rates in patients with stroke treated with bridging therapy
2017.
Mueller, Lukas A., Pult, F., Meisterernst, J., Heldner, M. R., Mono, M. L., Kurmann, R., Buehlmann, …
European Journal of Neurology.
24
:
1016–1021
Transcriptomic analysis of Olea europaea L. Roots during the Verticillium dahliae early infection process
2017.
Jiménez-Ruiz, J., Leyva-Pérez, M. DLO, Schilirò, E., Barroso, J. B., Bombarely, A., Mueller, Luka…
The Plant Genome.
10
:
0–0
De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus
2017.
Montero-Pau, J., Blanca, J., Bombarely, A., Ziarsolo, P., Esteras, C., Martí-Gómez, C., Ferriol, M…
Plant Biotechnology Journal.
16
:
1161–1171
 

Contact:

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