Publications – Lukas Mueller

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
:
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
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
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 Mukht…
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., C…
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.
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
:
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
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
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
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
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.
BMC Genomics.
17
:
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.,…
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
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
:
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…
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, …
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, …
PeerJ.
2015
:
e793–e793
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…
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, …
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., Muelle…
Planta.
241
:
179–191
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., Suzuk…
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.
Genome.
57
:
169–180
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, …
BMC Bioinformatics.
15
:
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…
BMC Plant Biology.
14
:
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.…
BMC Genomics.
14
:
51–51
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…
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.…
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.
BMC Genomics.
13
:
406–406
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.,…
:
220–225
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.,…
Nature.
485
:
635–641
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., F…
Proteomics.
12
:
761–774
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.…
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., Le…
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…
BMC Genomics.
12
:
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., Luca…
Nature.
463
:
763–768
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., Latendr…
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.
BMC Genomics.
11
:
142–142
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.,…
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,…
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 …
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., H…
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.
Genetics.
174
:
1407–1420
Save our data!
2006.
Stein, L. D., Eleavis, W. D., Gessler, D. D., Huala, E., Lawrence, C. J., Main, D., Mueller, Lukas A…
SCIENTIST.
20
:
24–25
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.
Genetics.
172
:
2529–2540
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, …
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…
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…
BMC Plant Biology.
5
:
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, …
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, Luka…
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., Hua…
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., Lambrec…
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., Ki…
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.
Planta.
203
:
260–263
Characterization of a tyrosinase from Amanita muscaria involved in betalain biosynthesis
1996.
Mueller, Lukas A., Hinz, U., Zrÿd, J. P.
Phytochemistry.
42
:
1511–1515

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