Connecting Data for Consumer Preferences, Food Quality and Breeding in support of Market-oriented Breeding of Root, Tuber, and Banana Crops
2023.
Arnaud, E., Menda, N., Tran, T., Asiimwe, A., Kanaabi, M., Meghar, K., Forsythe, L., Kawuki, R., Ellebrock, B., Kayondo, I.S., Agbona, A., Zhang, X., Mendes, T., Laporte, M.A., Nakitto, M., Ssali, R.T., Asfaw, A., Uwimana, B., Ogbete, C.E., Makunde, G., Maraval, I., Mueller, Lukas A., Bouniol, A., Fauvelle, E., Dufour, D.
Journal of the Science of Food and Agriculture.
:
MangoBase: A Genomics Portal and Gene Expression Atlas for Mangifera indica
2023.
Gómez-Ollé, A., Bullones, A., Hormaza, J.I., Mueller, Lukas A., Fernandez-Pozo, N.
Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features
2022.
Shippy, T.D., Hosmani, P.S., Flores-Gonzalez, M., Mueller, Lukas A., Hunter, W.B., Brown, S.J., D'Elia, T., Saha, S.
Genomic identification, annotation, and comparative analysis of Vacuolar-type ATP synthase subunits in Diaphorina citri
2022.
Grace, R., Massimino, C., Shippy, T.D., Tank, W., Hosmani, P.S., Flores-Gonzalez, M., Mueller, Lukas A., Hunter, W.B., Benoit, J.B., Brown, S.J., D'Elia, T., Saha, S.
Ubiquitin-proteasome pathway annotation in Diaphorina citri can reveal potential targets for RNAi-based pest management
2022.
Tank, W., Shippy, T., Thate, A., Massimino, C., Hosmani, P.S., Flores-Gonzalez, M., Mueller, Lukas A., Hunter, W.B., Brown, S.J., D'Elia, T., Saha, S.
Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri
2022.
Shippy, T.D., Miller, S., Tamayo, B., Hosmani, P.S., Flores-Gonzalez, M., Mueller, Lukas A., Hunter, W.B., Brown, S.J., D'Elia, T., Saha, S.
Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae)
2022.
Reynolds, M., de Oliveira, L., Vosburg, C., Paris, T., Massimino, C., Norus, J., Ortiz, Y., Espino, M., Davis, N., Masse, R., Neiman, A., Holcomb, R., Gervais, K., Kemp, M., Hoang, M., Shippy, T.D., Hosmani, P.S., Flores-Gonzalez, M., Pelz-Stelinski, K., Qureshi, J.A., Mueller, Lukas A., Hunter, W.B., Benoit, J.B., Brown, S.J., D'Elia, T., Saha, S.
Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress.
2022.
Nicolas, P., Shinozaki, Y., Powell, A., Philippe, G., Snyder, S.I., Bao, K., Zheng, Y., Xu, Y., Courtney, L., Vrebalov, J., Casteel, C.L., Mueller, Lukas A., Fei, Zhangjun, Giovannoni, James J., Rose, J.K.C., Catalá, Carmen
Current status and impending progress for cassava structural genomics.
2022.
Lyons, J.B., Bredeson, J.V., Mansfeld, B.N., Bauchet, G.J., Berry, J., Boyher, A., Mueller, Lukas A., Rokhsar, D.S., Bart, R.S.
Plant Mol Biol..
109
:
177–191
Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae.
2022.
Powell, A.F., Zhang, J., Hauser, D., Vilela, J.A., Hu, A., Gates, D.J., Mueller, Lukas A., Li, Fay-Wei, Strickler, S.R., Smith, S.D.
Graph pangenome captures missing heritability and empowers tomato breeding.
2022.
Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., Wu, Y., Cheng, L., Fang, Y., Wu, K., Zhang, J., Lyu, H., Lin, T., Gao, Q., Saha, S., Mueller, Lukas A., Fei, Zhangjun, Städler, T., Xu, S., Zhang, Z., Speed, D., Huang, S.
Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn’s disease
2022.
Zhang, S., Morgan, X., Dogan, B., Martin, F.P., Strickler, S., Oka, A., Herzog, J., Liu, B., Dowd, S.E., Huttenhower, C., Pichaud, M., Dogan, E.I., Satsangi, J., Longman, R., Yantiss, R., Mueller, Lukas A., Scherl, E.J., Sartor, R.B., Simpson, K.W.
Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data
2022.
Mann, M., Saha, S., Cicero, J.M., Pitino, M., Moulton, K., Hunter, W.B., Cano, L.M., Mueller, Lukas A., Heck, M.
A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity.
2022.
Powell, A.F., Feder, A., Li, J., Schmidt, M.H., Courtney, L., Alseekh, S., Jobson, E.M., Vogel, A., Xu, Y., Lyon, D., Dumschott, K., McHale, M., Sulpice, R., Bao, K., Lal, R., Duhan, A., Hallab, A., Denton, A.K., Bolger, M.E., Fernie, A.R., Hind, S.R., Mueller, Lukas A., Martin, Gregory B., Fei, Zhangjun, Martin, C., Giovannoni, James J., Strickler, S.R., Usadel, B.
Breedbase: a digital ecosystem for modern plant breeding.
2022.
Morales, N., Ogbonna, A.C., Ellerbrock, B.J., Bauchet, G.J., Tantikanjana, T., Tecle, I.Y., Powell, A.F., Lyon, D., Menda, N., Simoes, C.C., Saha, S., Hosmani, P., Flores, M., Panitz, N., Preble, R.S., Agbona, A., Rabbi, I., Kulakow, P., Peteti, P., Kawuki, R., Esuma, W., Kanaabi, M., Chelangat, D.M., Uba, E., Olojede, A., Onyeka, J., Shah, T., Karanja, M., Egesi, C., Tufan, H., Paterne, A., Asfaw, A., Jannink, J.L., Wolfe, M., Birkett, C.L., Waring, D.J., Hershberger, J.M., Gore, M.A., Robbins, K.R., Rife, T., Courtney, C., Poland, J., Arnaud, E., Laporte, M.A., Kulembeka, H., Salum, K., Mrema, E., Brown, A., Bayo, S., Uwimana, B., Akech, V., Yencho, C., de Boeck, B., Campos, H., Swennen, R., Edwards, J.D., Mueller, Lukas A.
Chromosome length genome assembly of the redbanded stink bug, Piezodorus guildinii (Westwood)
2022.
Saha, S, Allen, K.C., Mueller, Lukas A., Reddy, G.V.P., Perera, O.P.
Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication.
2021.
Ogbonna, A.C., Braatz de Andrade, L.R., Mueller, Lukas A., de Oliveira, E.J., Bauchet, G.J.
Theor Appl Genet..
134
:
1343–1362
Can Cross-Country Genomic Predictions Be a Reasonable Strategy to Support Germplasm Exchange? – A Case Study With Hydrogen Cyanide in Cassava
2021.
Torres, L.G., de Oliveira, E.J., Ogbonna, A.C., Bauchet, G.J., Mueller, Lukas A., Azevedo, C.F., Silva, F.F.E., Simiqueli, G.F., de Resende, M.D.V.
Front Plant Sci..
12
:
742638
A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)
2021.
Ogbonna, A.C., Ramu, P., Esuma, W., Nandudu, L., Morales, N., Powell, A., Kawuki, R., Bauchet, G., Jannink, J.L., Mueller, Lukas A.
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook
2021.
Foerster, H., Battey, J.N.D., Sierro, N., Ivanov, N.V., Mueller, Lukas A.
Brief Bioinform..
22
:
bbaa136
The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago.
2021.
Raharimalala, N., Rombauts, S., McCarthy, A., Garavito, A., Orozco-Arias, S., Bellanger, L., Morales-Correa, A.Y., Froger, S., Michaux, S., Berry, V., Metairon, S., Fournier, C., Lepelley, M., Mueller, Lukas A., Couturon, E., Hamon, P., Rakotomalala, J.J., Descombes, P., Guyot, R., Crouzillat, D.
Annotation of segmentation pathway genes in the Asian citrus psyllid, Diaphorina citri
2021.
Miller, S., Shippy, T.D., Hosmani, P.S., Flores-Gonzalez, M., Mueller, Lukas A., Hunter, W.B., Brown, S.J., D’Elia, T., Saha, S.
The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality
2021.
Mango Genome Consortium, Bally, I.S.E., Bombarely, A., Chambers, A.H., Cohen, Y., Dillon, N.L., Innes, D.J., Islas-Osuna, M.A., Kuhn, D.N., Mueller, Lukas A., Ophir, R., Rambani, A., Sherman, A., Yan, H.
Current status and impending progress for cassava structural genomics
2021.
Lyons, J.B., Bredeson, J.V., Mansfeld, B.N., Bauchet, G.J., Berry, J., Boyher, A., Mueller, Lukas A., Rokhsar, D.S., Bart, R.S.
Large-scale GWAS using historical data identifies a conserved genetic architecture of cyanogenic glucosides content in cassava (Manihot esculenta Crantz.) root
2021.
Ogbonna, A.C., Braatz de Andrade, L.R., Rabbi, I.Y., Mueller, Lukas A., de Oliverira, E.J., Bauchet, G.J.
PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens
2020.
Fernandez-Pozo, N., Haas, F.B., Meyberg, R., Ullrich, K.K., Hiss, M., Perroud, P.F., Hanke, S., Kratz, V., Powell, A.F., Vesty, E.F., Daum, C.G., Zane, M., Lipzen, A., Sreedasyam, A., Grimwood, J., Coates, J.C., Barry, K., Schmutz, J., Mueller, Lukas A., Rensing, S.A.
Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding
2020.
Wang, X., Gao, L., Jiao, C., Stravoravdis, S., Hosmani, P.S., Saha, S., Zhang, J., Mainiero, S., Strickler, Susan, R., Catala, Carmen, Martin, Gregory, B., Mueller, Lukas A., Vrebalov, J., Giovannoni, James J., Wu, S., Fei, Zhangjun
Draft Genome Sequence Resource of the Citrus Stem-End Rot Fungal Pathogen Lasiodiplodia theobromae CITRA15
2020.
Zheng, Q., Ozbudak, E., Liu, G., Hosmani, P.S., Saha, S., Flores-Gonzales, M., Mueller, Lukas A., Rodrigues-Stuart, K., Dewdney, M.M., Lin, Y., Zhang, J., Carrillo-Tarazona, Y., Liu, B., Oliva, R., Ritenour, M., Cana, L.M.
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems
2020.
Arnaud, E., Laporte, M.A., Kim, S., Aubert, C., Leonelli, S., Miro, B., Cooper, L., Jaiswal, P., Kruseman, G., Shrestha, R., Buttigieg, P.L., Mungall, C.J., Bauchet, G., Mueller, Lukas A., Silverstein, K., Lafargue, A., Antezana, E., Devare, M., King, B.
High density genotype storage for plant breeding in the Chado schema of Breedbase
2020.
Morales, N., Bauchet, G.J., Tantikanjana, T, Powell, A.F., Ellerbrock, B.J., Tecle, I.Y., Mueller, Lukas A.
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., Howe, K.J., Moulton, K., Saha, S., Mueller, Lukas A., Hall, D.G., Shatters, R.G., Heck, Michelle L., Slupsky, C.M.
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., Mishra, B., Mukhtar, M.S., Scheffler, B.E., Scheffler, J.A., Mueller, Lukas A., Mansoor, S.
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., Strickler, S.R., Mueller, Lukas A., Rodrigues, R., Goncalves, L.S.A.
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.
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., Calaminos, V.C., Carceller, P., Cornut, G., Costa, B.V., Edwards, J.D., Mueller, Lukas A., BrAPI Consortium
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., Mueller, Lukas A., Blanca, J., Canizares, J., van der Knaap, E., Diez, M.J.
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., Mitrovic, E., Xu, Y., Strickler, S.R., Fernandez, N., Zhong, X., Polek, M., Godfrey, K.E., Giovannoni, James J., Mueller, Lukas A., Slupsky, C.M., Bruce, J.E., Heck, Michelle L.
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., Kumar, P., Erb, M., Petschenka, G., Gomez, J.M., Perfectti, F., Müller, C., Pires, J.C., Mueller, Lukas A., Jander, Georg
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., Polek, M., Godfrey, K.E., Mueller, Lukas A., Bruce, J.E., Heck, Michelle L., Slupsky, C.M.
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., Mansoor, S.
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., Birkett, C., Calaminos, V.C., Carceller, P., Cornut, G., Vasques C., Edwards, J.D., Finkers, R., Yanxin G.S., Ghaffar, M., Glaser, P., Guignon, V., Hok, P., Kilian, A., König, P., Lagare, J.E.B., Lange, M., Laporte, M-A, Larmande, P, LeBauer, D.S., Lyon, D.A., Marshall, D.S., Matthews, D., Milne, I., Mistry, N., Morales, N., Mueller, Lukas A., Neveu, P., Papoutsoglou, E., Pearce, B., Perez-Masias, I., Pommier, C., Ramírez-González, R.H., Rathore, A., Raquel, A.M., Raubach, S., Rife, T., Robbins, K., Rouard, M., Sarma, C., Scholz, U., Sempéré, G., Shaw, P.D., Simon, R., Soldevilla, N., Stephen, G., Sun, Q., Tovar, C., Uszynski, G., Verouden, M.
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., Powell, A.F., Futrell, S., Thannhauser, T.W., Fei, Zhangjun, Van Deynze, A.E., Mueller, Lukas A., Giovannoni, James J., Foolad, M.R.
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., Fournier, C., Moine, D., de Kochko, A., Yuyama, P. M., Vanzela, A. LL, Guyot, R.
Frontiers in Plant Science.
9
:
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.
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., Snyder, S. I., Martin, L. BB, Ruiz-May, E., Thannhauser, T. W., Chen, K., Domozych, D. S., Catala, Carmen, Fei, Zhangjun, Mueller, Lukas A., Giovannoni, James J., Rose, Jocelyn
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, M., Fischer, U., Mattle, H. P., Arnold, M., Mordasini, P., Gralla, J., Schroth, G., El-Koussy, M., Jung, S.
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, Lukas A., Mercado-Blanco, J., Luque, F.
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., Gómez, P., Jamilena, M., Mueller, Lukas A., Picó, B., Cañizares, J.
Plant Biotechnology Journal.
16
:
1161–1171
Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum
2017.
Naqvi, R. Z., Zaidi, S. SEA, Akhtar, K. P., Strickler, S., Woldemariam, M., Mishra, B., Shahid Mukhtar, M., Scheffler, B. E., Scheffler, J. A., Jander, Georg, Mueller, Lukas A., Asif, M., Mansoor, S.
Nature Scientific Reports.
7
:
Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
2017.
Saha, S., Hosmani, P. S., Villalobos-Ayala, K., Miller, S., Shippy, T., Flores, M., Rosendale, A., Cordola, C., Bell, T., Mann, H., DeAvila, G., DeAvila, D., Moore, Z., Buller, K., Ciolkevich, K., Nandyal, S., Mahoney, R., Van Voorhis, J., Dunlevy, M., Farrow, D., Hunter, D., Morgan, T., Shore, K., Guzman, V., Izsak, A., Dixon, D. E., Cridge, A., Cano, L., Cao, X., Jiang, H., Leng, N., Johnson, S., Cantarel, B. L., Richards, S., English, A., Shatters, R. G., Childers, C., Chen, M. J., Hunter, W., Heck, Michelle L., Mueller, Lukas A., Munoz-Torres, M., Nelson, D., Poelchau, M. F., Benoit, J. B., Wiersma-Koch, H., D'Elia, T., Brown, S. J.
Database : the journal of biological databases and curation.
2017
:
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.
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, F., Hurst, R., White, B., Kernodle, S. P., Bromley, J. R., Sanchez-Tamburrino, J. P., Lewis, R. S., Mueller, Lukas A.
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., Mattson, Neil S.
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., Christensen, S. A., Galis, I., Mueller, Lukas A., Jander, Georg, Hancock, R.
Journal of Experimental Botany.
68
:
4709–4723
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 A., Maccoss, M. J., Shatters, R. G., Heck, Michelle L.
PLOS One.
12
:
e0179531–e0179531
The Tomato Expression Atlas
2017.
Fernandez-Pozo, N., Zheng, Y., Snyder, S. I., Nicolas, P., Shinozaki, Y., Fei, Zhangjun, Catala, Carmen, Giovannoni, James J., Rose, J. KC, Mueller, Lukas A.
Bioinformatics (Oxford, England).
33
:
2397–2398
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
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.
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
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., Latendresse, M., Mueller, Lukas A., Ong, Q., Paley, S., Subhraveti, P., Weaver, D. S., Karp, P. D.
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., Borghi, L., Bruggmann, R., Bucher, M., D'Agostino, N., Davies, K., Druege, U., Dudareva, N., Egea-Cortines, M., Delledonne, M., Fernandez-Pozo, N., Franken, P., Grandont, L., Heslop-Harrison, J. S., Hintzsche, J., Johns, M., Koes, R., Lv, X., Lyons, E., Malla, D., Martinoia, E., Mattson, N. S., Morel, P., Mueller, Lukas A., Muhlemann, J., Nouri, E., Passeri, V., Pezzotti, M., Qi, Q., Reinhardt, D., Rich, M., Richert-Pöggeler, K. R., Robbins, T. P., Schatz, M. C., Schranz, M. E., Schuurink, R. C., Schwarzacher, T., Spelt, K., Tang, H., Urbanus, S. L., Vandenbussche, M., Vijverberg, K., Villarino, G. H., Warner, R. M., Weiss, J., Yue, Z., Zethof, J., Quattrocchio, F., Sims, T. L., Kuhlemeier, C.
Nature Plants.
2
:
16074–16074
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 A., Barrero, L. S.
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
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
An Endophyte Constructs Fungicide-Containing Extracellular Barriers for Its Host Plant
2015.
Soliman, S. SM, Greenwood, J. S., Bombarely, A., Mueller, Lukas A., Tsao, R., Mosser, D. D., Raizada, M. N.
Current Biology.
25
:
2570–2576
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, A., Fisher-York, T., Pujar, A., Foerster, H., Yan, A., Mueller, Lukas A.
Nucleic Acids Research.
43
:
D1036–D1041
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
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, Lukas A.
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
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., Meihls, L. N., Kaur, H., Huffaker, A., Mori, N., Degenhardt, J., Mueller, Lukas A., Jander, Georg
Plant Physiology.
169
:
1727–1743
The Genome Database for Rosaceae (GDR): Year 10 update
2014.
Jung, S., Ficklin, S. P., Lee, T., Cheng, C. H., Blenda, A., Zheng, P., Yu, J., Bombarely, A., Cho, I., Ru, S., Evans, K., Peace, C., Abbott, A. G., Mueller, Lukas A., Olmstead, M. A., Main, D.
Nucleic Acids Research.
42
:
D1237–D1244
Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta)
2014.
Perrois, C., Strickler, S. R., Mathieu, G., Lepelley, M., Bedon, L., Michaux, S., Husson, J., Mueller, Lukas A., Privat, I.
The Tomato Kinome and the Tomato Kinase Library ORFeome: Novel Resources for the Study of Kinases and Signal Transduction in Tomato and Solanaceae Species
2014.
Singh, D. K., Calvino, M., Brauer, E. K., Fernandez-Pozo, N., Strickler, S., Yalamanchili, R., Suzuki, H., Aoki, K., Shibata, D., Stratmann, J. W., Popescu, G. V., Mueller, Lukas A., Popescu, S. C.
Molecular Plant-Microbe Interactions.
27
:
7–17
Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex
2014.
Labate, J. A., Robertson, L. D., Strickler, S. R., Mueller, Lukas A.
solGS: a web-based tool for genomic selection
2014.
Tecle, I. Y., Edwards, J. D., Menda, N., Egesi, C., Rabbi, I. Y., Kulakow, P., Kawuki, R., Jannink, J. L., Mueller, Lukas A.
Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins
2014.
Menda, N., Strickler, S. R., Edwards, J. D., Bombarely, A., Dunham, D. M., Martin, Gregory B., Mejia, L., Hutton, S. F., Havey, M. J., Maxwell, D. P., Mueller, Lukas A.
Molecular Phylogeny of Daucus (Apiaceae)
2013.
Spooner, D., Rojas, P., Bonierbale, M., Mueller, Lukas A., Srivastav, M., Senalik, D., Simon, P.
Systematic Botany.
38
:
850–857
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., Mueller, Lukas A.
Database : the journal of biological databases and curation.
2013
:
bat028–bat028
Linking the potato genome to the conserved ortholog set (COS) markers
2013.
Lindqvist-Kreuze, H., Cho, K., Portal, L., Rodríguez, F., Simon, R., Mueller, Lukas A., Spooner, D. M., Bonierbale, M.
Advances in tomato research in the post-genome era
2013.
Menda, N., Strickler, S. R., Mueller, Lukas A.
Plant Biotechnology.
30
:
243–256
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions
2013.
Xu, Y., Wang, J., Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W. J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., Min, J., Guo, X., Murat, F., Ham, B. K., Zhang, Z., Gao, S., Huang, M., Xu, Y., Zhong, S., Bombarely, A., Mueller, Lukas A., 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, James J., Li, Y., Fei, Zhangjun
Nature genetics.
45
:
51–58
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., Menda, N., Mueller, Lukas A., Mutschler, M. A., Loewen, S. A., Myers, J. R., Francis, D. M.
Journal of the American Society for Horticultural Science.
137
:
427–437
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective
2012.
Bombarely, A., Edwards, K. D., Sanchez-Tamburrino, J., Mueller, Lukas A.
Designing a transcriptome next-generation sequencing project for a nonmodel plant species1
2012.
Strickler, S. R., Bombarely, A., Mueller, Lukas A.
American Journal of Botany.
99
:
257–266
Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes
2012.
Arnaud, E., Cooper, L., Shrestha, R., Menda, N., Nelson, R. T., Matteis, L., Skofic, M., Bastow, R., Jaiswal, P., Mueller, Lukas A., McLaren, G.
Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)
2012.
Cai, D., Rodríguez, F., Teng, Y., Ané, C., Bonierbale, M., Mueller, Lukas A., Spooner, D. M.
BMC Evolutionary Biology.
12
:
70–70
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, Lukas A., Martin, Gregory B.
Molecular Plant-Microbe Interactions.
25
:
1523–1530
The tomato genome sequence provides insights into fleshy fruit evolution
2012.
Sato, S., Tabata, S., Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y., Shibata, D., Aoki, K., Egholm, M., Knight, J., Bogden, R., Li, C., Shuang, Y., Xu, X., Pan, S., Cheng, S., Liu, X., Ren, Y., Wang, J., Albiero, A., Dal Pero, F., Todesco, S., Van Eck, Joyce, Buels, R. M., Bombarely, A., Gosselin, J. R., Huang, M., Leto, J. A., Menda, N., Strickler, S., Mao, L., Gao, S., Tecle, I. Y., York, T., Zheng, Y., Vrebalov, J. T., Lee, J., Zhong, S., Mueller, Lukas A., Stiekema, W. J., Ribeca, P., Alioto, T., Yang, W., Huang, S., Du, Y., Zhang, Z., Gao, J., Guo, Y., Wang, X., Li, Y., He, J., Li, C., Cheng, Z., Zuo, J., Ren, J., Zhao, J., Yan, L., Jiang, H., Wang, B., Li, H., Li, Z., Fu, F., Chen, B., Han, B., Feng, Q., Fan, D., Wang, Y., Ling, H., Xue, Y., Ware, D., Richard McCombie, W., Lippman, Z. B., Chia, J. M., Jiang, K., Pasternak, S., Gelley, L., Kramer, M., Anderson, L. K., Chang, S. B., Royer, S. M., Shearer, L. A., Stack, S. M., Rose, Jocelyn, Xu, Y., Eannetta, N., Matas, A. J., McQuinn, R., Tanksley, S. D., Camara, F., Guigó, R., Rombauts, S., Fawcett, J., Van de Peer, Y., Zamir, D., Liang, C., Spannagl, M., Gundlach, H., Bruggmann, R., Mayer, K., Jia, Z., Zhang, J., Ye, Z., Bishop, G. J., Butcher, S., Lopez-Cobollo, R., Buchan, D., Filippis, I., Abbott, J., Dixit, R., Singh, M., Singh, A., Kumar Pal, J., Pandit, A., Kumar Singh, P., Kumar Mahato, A., Dogra, V., Gaikwad, K., Raj Sharma, T., Mohapatra, T., Kumar Singh, N., Causse, M., Rothan, C., Schiex, T., Noirot, C., Bellec, A., Klopp, C., Delalande, C., Berges, H., Mariette, J., Frasse, P., Vautrin, S., Zouine, M., Latché, A., Rousseau, C., Regad, F., Pech, J. C., Philippot, M., Bouzayen, M., Pericard, P., Osorio, S., Fernandez del Carmen, A., Monforte, A., Granell, A., Fernandez-Muñoz, R., Conte, M., Lichtenstein, G., Carrari, F., De Bellis, G., Fuligni, F., Peano, C., Grandillo, S., Termolino, P., Pietrella, M., Fantini, E., Falcone, G., Fiore, A., Giuliano, G., Lopez, L., Facella, P., Perrotta, G., Daddiego, L., Bryan, G., Orozco, M., Pastor, X., Torrents, D., van Schriek, M. GM, Feron, R. MC, van Oeveren, J., de Heer, P., daPonte, L., Jacobs-Oomen, S., Cariaso, M., Prins, M., van Eijk, M. JT, Janssen, A., van Haaren, M. JJ, Jo, S. H., Kim, J., Kwon, S. Y., Kim, S., Koo, D. H., Lee, S., Hur, C. G., Clouser, C., Rico, A., Hallab, A., Gebhardt, C., Klee, K., Jöcker, A., Warfsmann, J., Göbel, U., Kawamura, S., Yano, K., Sherman, J. D., Fukuoka, H., Negoro, S., Bhutty, S., Chowdhury, P., Chattopadhyay, D., Datema, E., Smit, S., Schijlen, E. GWM, van de Belt, J., van Haarst, J. C., Peters, S. A., van Staveren, M. J., Henkens, M. HC, Mooyman, P. JW, Hesselink, T., van Ham, R. CHJ, Jiang, G., Droege, M., Choi, D., Kang, B. C., Dong Kim, B., Park, M., Kim, S., Yeom, S. I., Lee, Y. H., Choi, Y. D., Li, G., Gao, J., Liu, Y., Huang, S., Fernandez-Pedrosa, V., Collado, C., Zuñiga, S., Wang, G., Cade, R., Dietrich, R. A., Rogers, J., Knapp, S., Fei, Zhangjun, White, R. A., Thannhauser, T. W., Giovannoni, James J., Angel Botella, M., Gilbert, L., Gonzalez, R., Luis Goicoechea, J., Yu, Y., Kudrna, D., Collura, K., Wissotski, M., Wing, R., Schoof, H., Meyers, B. C., Bala Gurazada, A., Green, P. J., Mathur, S., Vyas, S., Solanke, A. U., Kumar, R., Gupta, V., Sharma, A. K., Khurana, P., Khurana, J. P., Tyagi, A. K., Dalmay, T., Mohorianu, I., Walts, B., Chamala, S., Brad Barbazuk, W., Li, J., Guo, H., Lee, T. H., Wang, Y., Zhang, D., Paterson, A. H., Wang, X., Tang, H., Barone, A., Luisa Chiusano, M., Raffaella Ercolano, M., D’Agostino, N., Di Filippo, M., Traini, A., Sanseverino, W., Frusciante, L., Seymour, G. B., Elharam, M., Fu, Y., Hua, A., Kenton, S., Lewis, J., Lin, S., Najar, F., Lai, H., Qin, B., Qu, C., Shi, R., White, D., White, J., Xing, Y., Yang, K., Yi, J., Yao, Z., Zhou, L., Roe, B. A., Vezzi, A., D’Angelo, M., Zimbello, R., Schiavon, R., Caniato, E., Rigobello, C., Campagna, D., Vitulo, N., Valle, G., Nelson, D. R., De Paoli, E., Szinay, D., de Jong, H. H., Bai, Y., Visser, R. GF, Klein Lankhorst, R. M., Beasley, H., McLaren, K., Nicholson, C., Riddle, C., Gianese, G., Sato, S., Tabata, S., Mueller, Lukas A., Huang, S., Du, Y., Li, C., Cheng, Z., Zuo, J., Han, B., Wang, Y., Ling, H., Xue, Y., Ware, D., Richard McCombie, W., Lippman, Z. B., Stack, S. M., Tanksley, S. D., Van de Peer, Y., Mayer, K., Bishop, G. J., Butcher, S., Kumar Singh, N., Schiex, T., Bouzayen, M., Granell, A., Carrari, F., De Bellis, G., Giuliano, G., Bryan, G., van Eijk, M. JT, Fukuoka, H., Chattopadhyay, D., van Ham, R. CHJ, Choi, D., Rogers, J., Fei, Zhangjun, Giovannoni, James J., Wing, R., Schoof, H., Meyers, B. C., Khurana, J. P., Tyagi, A. K., Dalmay, T., Paterson, A. H., Wang, X., Frusciante, L., Seymour, G. B., Roe, B. A., Valle, G., de Jong, H. H., Klein Lankhorst, R. M.
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, Lukas A., Thannhauser, T. W., Zhang, S., Fei, Zhangjun, Giovannoni, James J., Rose, Jocelyn
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, Lukas A., Main, D.
Database : the journal of biological databases and curation.
2011
:
bar051–bar051
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., Mueller, Lukas A.
Nucleic Acids Research.
39
:
D1149–D1155
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, Lukas A., Joët, T., Pot, D., Foucrier, S., Dussert, S., Leroy, T., Journot, L., de Kochko, A., Campa, C., Combes, M. C., Lashermes, P., Bertrand, B.
Genome sequencing and analysis of the model grass Brachypodium distachyon
2010.
Vogel, J. P., Garvin, D. F., Mockler, T. C., Schmutz, J., Rokhsar, D., Bevan, M. W., Barry, K., Lucas, S., Harmon-Smoth, M., Lail, K., Tice, H., Grimwood, J., McKenzie, N., Huo, N., Gu, Y. Q., Lazo, G. R., Anderson, O. D., You, F. M., Luo, M. C., Dvorak, J., Wright, J., Febrer, M., Idziak, D., Hasterok, R., Lindquist, E., Wang, M., Fox, S. E., Priest, H. D., Filichkin, S. A., Givan, S. A., Bryant, D. W., Chang, J. H., Wu, H., Wu, W., Hsia, A. P., Schnable, P. S., Kalyanaraman, A., Baarbazuk, B., Michael, T. P., Hazen, S. P., Bragg, J. N., Laudencia-Chingcuanco, D., Weng, Y., Haberer, G., Spannagl, M., Mayer, K., Rattei, T., Mitros, T., Lee, S. J., Rose, Jocelyn, Mueller, Lukas A., York, T. L., Wicker, T., Buchmann, J. P., Tanskanen, J., Schulman, A. H., Gundlach, H., de Oliveira, A. C., Maia, L. DC, Belknap, W., Jiang, N., Lai, J., Zhu, L., Ma, J., Sun, C., Pritham, E., Salse, J., Murat, F., Abrouk, M., Bruggmann, R., Messing, J., Fahlgren, N., Sullivan, C. M., Carrington, J. C., Chapman, E. J., May, G. D., Zhai, J., Ganssmann, M., Gurazada, S. GR, German, M., Meyers, B. C., Green, P. J., Tyler, L., Wu, J., Thomson, J., Chen, S., Scheller, H. V., Harholt, J., Ulvskov, P., Kimbrel, J. A., Bartley, L. E., Cao, P., Jung, K. H., Sharma, M. K., Vega-Sanchez, M., Ronald, P., Dardick, C. D., De Bodt, S., Verelst, W., Inze, D., Heese, M., Schnittger, A., Yang, X., Kalluri, U. C., Tuskan, G. A., Hua, Z., Vierstra, R. D., Cui, Y., Ouyang, S., Sun, Q., Liu, Z., Yilmaz, A., Grotewold, E., Sibout, R., Hematy, K., Mouille, G., Hoefte, H., Pelloux, J., O'Connor, D., Schbnable, J., Rowe, S., Harmon, F., Cass, C. L., Sedbrook, J. C., Byrne, M. E., Walsh, S., Higgins, J., Li, P., Brutnell, T., Unver, T., Budak, H., Belcram, H., Charles, M., Chalhoub, B., Baxter, I., Initiative, I. B.
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., Dreher, K., Karthikeyan, A., Chi, A., Pujar, A., Caspi, R., Karp, P., Kirkup, V., Latendresse, M., Lee, C., Mueller, Lukas A., Muller, R., Rhee, S. Y.
Plant Physiology.
153
:
1479–1491
Analysis of Ultra Low Genome Conservation in Clostridium difficile
2010.
Scaria, J., Ponnala, L., Janvilisri, T., Yan, W., Mueller, Lukas A., Chang, Yung-Fu
PLOS One.
5
:
e15147–e15147
TobEA: An atlas of tobacco gene expression from seed to senescence
2010.
Edwards, K. D., Bombarely, A., Story, G. W., Allen, F., Mueller, Lukas A., Coates, S. A., Jones, L.
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., Mueller, Lukas A.
BMC Bioinformatics.
11
:
525–525
A Snapshot of the Emerging Tomato Genome Sequence
2009.
Mueller, Lukas A., Lankhorst, R. K., Tanksley, S. D., Giovannoni, James J., White, R., Vrebalov, J., Fei, Zhangjun, Van Eck, Joyce, Buels, R., Mills, A. A., Menda, N., Tecle, I. Y., Bombarely, A., Stack, S., Royer, S. M., Chang, S. B., Shearer, L. A., Kim, Beum Jun, Jo, S. H., Hur, C. G., Choi, D., Li, C. B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, Xiaolong, Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G. B., Bishop, G. J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, Charles Frederick, Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A. U., Kumar, R., Gupta, V., Sharma, A. K., Khurana, P., Khurana, J. P., Tyagi, A., Sarita, Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I. A., Gaikwad, K., Sharma, T. R., Mohapatra, T., Singh, N. K., Szinay, D., de Jong, H., Peters, Scott, van Staveren, M., Datema, E., Fiers, M. WEJ, van Ham, R. CHJ, Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M. A., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, N., Chiusano, M. L., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Joecker, A., Bruggmann, R., Spannagl, M., Mayer, K. XF, Guigo, R., Camara, F., Rombauts, S., Fawcett, J. A., Van de Peer, Y., Knapp, S., Zamir, D., Stiekema, W.
The Plant Genome.
2
:
78–92
An EST database for Liriodendron tulipifera L. floral buds: The first EST resource for functional and comparative genomics in Liriodendron
2008.
Liang, H., Carlson, J. E., Leebens-Mack, J. H., Wall, P. K., Mueller, Lukas A., Buzgo, M., Landherr, L. L., Hu, Y., DiLoreto, D. S., Ilut, D. C., Field, D., Tanksley, S. D., Ma, H., DePamphilis, C. W.
Tree Genetics & Genomes.
4
:
419–433
The SGN comparative map viewer
2008.
Mueller, Lukas A., Mills, A. A., Skwarecki, B., Buels, R. M., Menda, N., Tanksley, S. D.
Bioinformatics (Oxford, England).
24
:
422–423
A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes
2008.
Menda, N., Buels, R. M., Tecle, I., Mueller, Lukas A.
Plant Physiology.
147
:
1788–1799
Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato
2008.
Datema, E., Mueller, Lukas A., Buels, R., Giovannoni, James J., Visser, R. GF, Stiekema, W. J., Van Ham, R. CHJ
BMC Plant Biology.
8
:
34–34
EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot
2006.
Carlson, J. E., Leebens-Mack, J. H., Wall, P. K., Zahn, L. M., Mueller, Lukas A., Landherr, L. L., Hu, Y., Ilut, D. C., Arrington, J. M., Choirean, S., Becker, A., Field, D., Tanksley, S. D., Ma, H., DePamphilis, C. W.
Plant Molecular Biology.
62
:
351–369
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, Lukas A., Crouzillat, D., Pétiard, V., Tanksley, S. D.
Save our data!
2006.
Stein, L. D., Eleavis, W. D., Gessler, D. D., Huala, E., Lawrence, C. J., Main, D., Mueller, Lukas A., Rhee, S. Y., Rokhsar, D. S.
Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome
2006.
Wang, Y., Tang, X., Cheng, Z., Mueller, Lukas A., Giovannoni, James J., Tanksley, S. D.
PatMatch: a program for finding patterns in peptide and nucleotide sequences
2005.
Yan, T., Yoo, D., Berardini, T. Z., Mueller, Lukas A., Weems, D. C., Weng, S., Cherry, J. M., Rhee, S. Y.
Nucleic Acids Research.
33
:
W262–W266
The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond
2005.
Mueller, Lukas A., Solow, T. H., Taylor, N., Skwarecki, B., Buels, R., Binns, J., Lin, C., Wright, M. H., Ahrens, R., Wang, Yi, Herbst, E. V., Keyder, E. R., Menda, N., Zamir, D., Tanksley, S. D.
Plant Physiology.
138
:
1310–1317
MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research
2005.
Zhang, P., Foerster, H., Tissier, C. P., Mueller, Lukas A., Paley, S., Karp, P. D., Rhee, S. Y.
Plant Physiology.
138
:
27–37
Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts
2005.
Lin, C., Mueller, Lukas A., Carthy, J. M., Crouzillat, D., Pétiard, V., Tanksley, S. D.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.
112
:
114–130
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, Lukas A., Tanksley, S. D.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.
112
:
72–84
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, Lukas 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., Leebens-Mack, J. H.
Querying and computing with BioCyc databases
2005.
Krummenacker, M., Paley, S., Mueller, Lukas A., Yan, T., Karp, P. D.
Bioinformatics (Oxford, England).
21
:
3454–3455
The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL)
2005.
Mueller, Lukas A., Tanskley, S. D., Giovannoni, James J., Van Eck, Joyce, 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., Guiliano, G., Frusciante, L., Causse, M., Zamir, D.
Comparative and Functional Genomics.
6
:
153–158
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, Lukas A., Yoon, J., Doyle, A., Lander, G., Moseyko, N., Yoo, D., Xu, I., Zoeckler, B., Montoya, M., Miller, N., Weems, D., Rhee, S. Y.
Plant Physiology.
135
:
745–755
AraCyc: A Biochemical Pathway Database for Arabidopsis
2003.
Mueller, Lukas A., Zhang, P., Rhee, S. Y.
Plant Physiology.
132
:
453–460
A Sequence-Based Map of Arabidopsis Genes with Mutant Phenotypes
2003.
Meinke, D. W., Meinke, L. K., Showalter, T. C., Schissel, A. M., Mueller, Lukas A., Tzafrir, I.
Plant Physiology.
131
:
409–418
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, Lukas A., Mundodi, S., Reiser, L., Tacklind, J., Weems, D. C., Wu, Y., Xu, I., Yoo, D., Yoon, J., Zhang, P.
Nucleic Acids Research.
31
:
224–228
Differential aggregation of the Trembler and Trembler J mutants of peripheral myelin protein 22
2002.
Tobler, A. R., Liu, N., Mueller, Lukas A., Shooter, E. M.
Proceedings of the National Academy of Sciences.
99
:
483–488
StressDB: A Locally Installable Web-Based Relational Microarray Database Designed for Small User Communities
2002.
Mitra, M., Shah, N., Mueller, Lukas A., Pin, S., Fedoroff, N.
Comparative and Functional Genomics.
3
:
91–96
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, Lukas A., Mundodi, S., Reiser, L., Rhee, S. Y., Scholl, R., Tacklind, J., Weems, D. C., Wu, Y., Xu, I., Yoo, D., Yoon, J., Zhang, P.
Functional and Integrative Genomics.
2
:
239–253
Surviving in a sea of data: a survey of plant genome data resource and issues in building data management systems
2002.
Reiser, L., Mueller, Lukas A., Seung, Y. R.
Plant Molecular Biology.
48
:
59–74
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. W., Garcia-Hernandez, M., Weems, D., Reiser, L., LaFond, F., Hanley, D., Kiphart, D., Zhuang, M., Huang, W., Mueller, Lukas A., Bhattacharyya, D., Bhaya, D., Sobral, B. W., Beavis, W., Meinke, D. W., Town, C. D., Somerville, C., Rhee, S. Y.
Nucleic Acids Research.
29
:
102–105
Chapter Fourteen Models for vacuolar sequestration of anthocyanins
2001.
Mueller, Lukas A., Walbot, V.
Recent Advances in Phytochemistry.
35
:
297–312
AN9, a Petunia Glutathione S -Transferase Required for Anthocyanin Sequestration, Is a Flavonoid-Binding Protein
2000.
Mueller, Lukas A., Goodman, C. D., Silady, R. A., Walbot, V.
Plant Physiology.
123
:
1561–1570
The formation of betalamic acid and muscaflavin by recombinant dopa-dioxygenase from Amanita
1997.
Mueller, Lukas A., Hinz, U., Zryd, J. P.
Phytochemistry.
44
:
567–569
Biochemical complementation of the betalain biosynthetic pathway in Portulaca grandiflora by a fungal 3,4-dihydroxyphenylalanine dioxygenase
1997.
Mueller, Lukas A., Hinz, U., Uzé, M., Sautter, C., Zryd, J. P.
Characterization of a tyrosinase from Amanita muscaria involved in betalain biosynthesis
1996.
Mueller, Lukas A., Hinz, U., Zrÿd, J. P.
Phytochemistry.
42
:
1511–1515
