Staff Researchers
Hired Personnel and Interns
2022
- Fernadez-Pozo N*, Bombarely A (2022) “EasyGDB, easy system to implement a low maintenance and customizable genomics portal”. Bioinformatics, btac412, https://doi.org/10.1093/bioinformatics/btac412.
- Pezzi PH, Guzman-Rodriguez S, Giudicelli GC, Turchetto C, Bombarely A, Freitas L* (2022). “A convoluted tale of hybridization: ecological speciation and introgression in Petunia species from a transitional zone in South America”. Perspectives in Plant Ecology, Evolution and Systematic, 56:125688. https://doi.org/10.1016/j.ppees.2022.125688
- Guzmán S, Giudicelli G, Turchetto C, Bombarely A, Freitas L*, 2022 “Is the answer blowing in the wind? What does neutral and under selection genetic polymorphism talk about population structure in a coastal species”. Molecular Ecology, 31:2847– 2864. https://doi.org/10.1111/mec.16441
- Fick A, Swart V, Backer R, Bombarely A, Engelbrecht J, van den Berg N*. Partially Resistant Avocado Rootstock Dusa® Shows Prolonged Upregulation of Nucleotide Binding-Leucine Rich Repeat Genes in Response to Phytophthora cinnamomi Frontiers in Plant Sciences, 13:793644. doi: 10.3389/fpls.2022.793644.
- Massa S*, Pagliarello R, Cemmi A, Di Sarcina I, Bombarely A, Demurtas OCC, Diretto G, Paolini F, Petzold E, Bliek M, Bennici E, Fiore AD, De Rossi P, Spelt C, Koes R, Quattrocchio F, Benvenuto E, 2022 “Modifying anthocyanins biosynthesisin tomato hairy roots: a test bed for plant resistance to ionizing radiation and antioxidant properties in space”. Frontiers in Plant Sciences, 13:830931. https://doi.org/10.3389/fpls.2022.830931
- Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsboll PJ, Pampoulie C, Ruiz-Lopez MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni C, Jarvis ED, Balint M*, European Reference Genome Atlas (ERGA) Consortium, 2022 “The era of reference genomes in conservation genomics.” Trends in Ecology & Evolution, 37(3):197-202. https://doi.org/10.1016/j.tree.2021.11.008
- Yan H, Haak DC, Li S, Huang L, Bombarely A*, 2022 “Exploring transposable elements-based markers to identify allelic variations underlying agronomic traits in rice”, Plant Communications, 3(3):100207. https://doi.org/10.1016/j.xplc.2021.100270.
- Giudicelli GC, Turchetto C, Guzman S, Teixeira MC, Petzold E, Bombarely A, Freitas LB*, 2022 “Genomic population reveals potential micro-refuge in South America grasslands”. Journal of Biogeography, 49:51-65. https://doi.org/10.1111/jbi.14277.
2021
- Friel J, Bombarely A, Fornell CD, Luque F, Fernández-Ocaña AM, 2021. Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L. Plants, 10(11): 2514. https://doi.org/10.3390/plants10112514
- Bombarely A, Doulis AG, Lambrou KK, Zioutis C, Margaritis E, Koubouris G, 2021. Elucidation of the Origin of the Monumental Olive Tree of Vouves in Crete, Greece. Plants 10(11): 2374. https://doi.org/10.3390/plants10112374
- Ziarsolo P, Hasing T, Hilario R, Garcia-Carpintero V, Blanca J, Bombarely A*, Cañizares J* (2021) K-seq, an affordable, reliable and open Klenow-NGS based genotyping technology. Plant Methods 17, 30, https://doi.org/10.1186/s13007-021-00733-6.
- Garzón-Martínez GA, García-Arias FL, Enciso-Rodríguez FE, Soto-Suárez M, González C, Bombarely A, Barrero LS, Osorio-Guarín JA. (2021) Validation of candidate genes in the Physalis peruviana-Fusarium oxysporum pathosystem using RT-qPCR. PeerJ, 9:e11135, 7717/peerj.11135
- Bally ISE, Bombarely A, Chambers AH*, Cohen Y, Dillon NL, Eshed R, Innes DJ, Shalom MI, Islas-Osuna MA, Kuhn DN, Mueller LA, Ophir R, Rambani A, Rozen A, Sherman A, Yan H, (2021) The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality. BMC Plant Biology 21, 108. https://doi.org/10.1186/s12870-021-02858-1
- Caballero-Villalobos L, Silva-Arias GA, Giudicelli GC, Petzold E, Turchetto C, Bombarely A, Freitas LB*. (2021) Population demography in contact zones of two plant species with strong morphological and ecological differentiation. Botanical Journal of the Linnean Society, 196, 1:00-122, https://doi.org/10.1093/botlinnean/boaa091.
- Cucinotta M, Cavalleri A, Guazzotti A, Manrique S, Bombarely A, Oliveto S, Biffo S, Weijers D, Kater M, Colombo L* (2021) Auxin-independent MONOPTEROS function during ovule development. Current Opinion in Plant Biology, 31 (4), 892-899, https://doi.org/10.1016/j.cub.2020.11.026.
2020
- Yan H, Bombarely A, Li S* (2020) DeepTE a computational method for de novo classification of transposons with convolutional neural network. Bioinformatics, btaa 519, https://doi.org/10.1093/bioinformatics/btaa519.
- Huang L, Feng G, Yan H, Zhang Z, Bushman BS, Wang JP, Bombarely A, Li M, Yang Z, Nie G, Xie W, Xu L, Chen P, Zhao X, Jiang W, Zhang X* (2020) Assembly of the orchardgrass genome provides insights into its genome evolution and flowering regulation. Plant biotechnology Journal 18 (2): 373-388 https://doi.org/10.1111/pbi.13205.
- Pombo MA, Rosli HG, Fernandez-Pozo N, Bombarely A* (2020) Nicotiana benthamiana, A Popular Model for Genome Evolution and Plant–Pathogen Interactions. The Tobacco Genome Book, 231-247 – Compendium of Plant Genomes. Springer, Berlin, Heidelberg.
- Jimenez-Ruiz J, Ramírez-Tejero JA, Fernandez-Pozo N, Leyva-Perez MO, Yan H, De la Rosa R, Belaj A, Montes E, Rodríguez-Ariza MO, Navarro F, Barroso JB, Beuzon CR, Valpuesta V, Bombarely A*, Luque F* (2020) The phenotypic diversity of the olive tree (Olea europaea L.) domestication is driven by transposon activity. The Plant Genome 13:e20010 https://doi.org/10.1002/tpg2.20010.
2019
- Talavera A, Soorni A, Bombarely A, Matas AJ, Hormaza JI* (2019) Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana). Scientific reports 9 (1), 20137. doi:10.1038/s41598-019-56526-4
- Gramazio P, Yan H, Hasing T, Vilanova S, Prohens J, Bombarely A* (2019) Whole-genome resequencing of seven eggplant (Solanum melongena) and one wild relative (S. incanum) accessions provides new insights and breeding tools for eggplant enhancement. Frontiers in Plant Science 10:1220. doi:10.3389/fpls.2019.01220
- Cui C, Herlihy JH, Bombarely A, McDowell JM, Haak DC* (2019) Draft assembly of Phytopthora capsici from long-read sequencing uncovers complexity. Molecular Plant-Microbe Interactions 32:12, 1559-1563 https://doi.org/10.1094/MPMI-04-19-0103-TA.
- Hasing T, Rinaldi E, Manrique S, Colombo L, Haak DC, Zaitlin D, Bombarely A* (2019) Extensive phenotypic diversity in the cultivated Florist’s Gloxinia, Sinningia speciosa (Lodd.) Hiern, is derived from the domestication of a single founder population. Plants, People, Planet 1: 363– 374 https://doi.org/10.1002/ppp3.10065
- Yan H, Bombarely A, Xu B, Frazier TP, Zhang X, Chen J, Feng G, Wang C, Chen P, Cui C, Li Q, Zhao B, Huang L* (2019) Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation. Journal Experimental Botany erz325, https://doi.org/10.1093/jxb/erz325
- Soorni A, Borna T, Alemardan A, Chakrabarti M, Hunt A, Bombarely A* (2019) Transcriptome Landscape Variation in the Genus Thymus. Genes 10(8): 620. https://doi.org/10.3390/genes10080620
- Jung H, Winefield C, Bombarely A, Prentis P, Waterhouse P* (2019) Tools and strategies for long-read sequencing and de-novo assembly of plant genomes. Trend in Plant Science 24 (8): 700-724. https://doi.org/10.1016/j.tplants.2019.05.003
- Manrique S, Friel J, Gramazio P, Hasing T, Ezquer I, Bombarely A* (2019) Genetic Insights of the Modification of the Pre-Fertilization Mechanisms during Plant Domestication. Journal of Experimental Botany 70 (11), 3007-3019. https://doi.org/10.1093/jxb/erz231
- Hu Y, Resende M, Bombarely A, Brym M, Bassil E, Chambers A* (2019) Genomics-Based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and genotyping by sequencing. Scientific reports 9 (1), 3416. https://doi.org/10.1038/s41598-019-40144-1
2018
- Bally J, Jung H, Mortimer C, Naim F, Philips JG, Hellens R, Bombarely A, Goodin MM, Waterhouse PM* (2018) The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons. Annual Review of Phytopathology 56:405-426, https://doi.org/10.1146/annurev-phyto-080417-050141
- Yan H, Bombarely A, Xu B, Fraizer TP, Wang C, Cheng P, Chen J, Hasing T, Cui C, Zhang XZ, Zhao B, Huang L* (2018) SiRNA regulates DNA methylation that interferes gene and lncRNA expression in the heterozygous polyploid switchgrass. Biotechnology for Biofuels 11:208, https://doi.org/10.1186/s13068-018-1202-0.
- Bombarely A* (2018) Roses for Darwin. Nature Plants – News & Views. Published: 15 June 2018. 10.1038/s41477-018-0195-9
- Blankers T. Oh KP, Bombarely A, Shaw KL*. (2018) Evolution of the Genomic Architecture in a Rapid Island Radiation: Mapping Chromosomal Rearrangements and Recombination Rate Variation. Genetics August 2018 209: 1329-1344. https://doi.org/10.1534/genetics.118.300894
- Foerster H, Bombarely A, Battey JND, Sierro N, Ivanov NV, Mueller LA*. (2018) SolCyc: A database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. Database volume 2018 01/01/2018 bay035 https://doi.org/10.1093/database/bay035.
- Montero-Pau J, Blanca J, Bombarely A, Ziarsolo P, Esteras C, Martí-Gómez C, Ferriol M, Gómez P, Jamilena M, Mueller L, Picó B, Cañizares J*. (2018). De-novo assembly of zucchini genome: a whole genome duplication associated with the origin of the Cucurbita Plant Biotechnology 16 (6): 1161-1171 DOI: 10.1111/pbi.12860
2017
- Soorni A, Fatahi R, Haak D, Salami SA, Bombarely A*. (2017). Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm by Genotyping-By-Sequencing Data. Scientific Reports 7:15668 doi:10.1038/s41598-017-15816-5
- Sanchez-Sevilla JF, Vallarino JG, Osorio S, Bombarely A, Pose D, Merchante C, Botella MA, Amaya I, Valpuesta V*. (2017) Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa). Scientific Reports 7:13737 doi:10.1038/s41598-017-14239-6
- Carlson KD, Fernandez-Pozo N, Bombarely A, Mueller LM, Madlung A* (2017) Genomic and transcriptomic natural variation in two populations of the allopolyploid Arabidopsis suecica. BMC Genomics 18 (1), 653; doi: 1186/s12864-017-4067-x
- Villarino G, Hu Q, Scanlon M, Mueller LA, Bombarely A, Mattson N*. (2017) Dissecting tissue-specific transcriptomic responses from leaf and roots under salt stress in Petunia hybrida Mitchell. Genes 8(8), 195; doi:10.3390/genes8080195.
- Zhao C, Lasses T, Bako L, Kong D, Zhao B, Chanda B, Bombarely A, Cruz-Ramírez A, Scheres B, Brunner A, Beers E* (2017) XYLEM NAC DOMAIN1: A potential angiosperm innovation regulating xylem differentiation through multiple conserved linear motifs interacting with RETINOBLASTOMA-RELATED. New Phytologist 216: 76-89 doi:10.1111/nph.14704.
- Sherman-Broyles S, Bombarely A, Doyle JJ*. (2017). Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies. Journal of Systematics and Evolution 55: 365–376. doi:10.1111/jse.12268.
- Edwards K, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans A, Bombarely A, Allen F, Hurst R, White B, Kernodle S, Bromley J, Sanchez-Tamburrino J.P., Lewis R, Mueller LA* (2017) Map-based cloning of homeologous loci implicated in nitrogen utilization efficiency enabled by an improved Nicotiana tabacum genome assembly. BMC Genomics 18:448. doi:10.1186/s12864-017-3791-6.
- Zimmers J, Thomas M, Yang L, Bombarely A, Mancuso M, Wojciechowski M, Smith J*. (2017) Species Boundaries in the Astragalus cusickii Complex Delimited using Molecular Phylogenetic Techniques. Molecular Phylogenetics and Evolution 114 :93-110. doi:10.1016/j.ympev.2017.06.004.
- Mizzotti C, Galliani B, Dreni L, Sommer H, Bombarely A, Masiero S* (2017) ERAMOSA controls lateral branching in snapdragon. Scientific Reports 7:41319 doi:10.1038/srep41319.
- Soorni A, Haak D, Zaitlin D, Bombarely A* (2017) Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data. BMC Genomics 18 (1):49 doi:10.1186/s12864-016-3412-9.
- Jiménez-Ruiz J, Leyva-Pérez MO, Schilirò E, Barroso JB, Bombarely A, Mueller LM, Mercado-Blanco J, Luque F* (2017) Transcriptomic analysis of the olive (Olea europaea L.)-Verticillium dahliae interaction during early root infection process. The Plant Genome 10(1) DOI: doi:10.3835/plantgenome2016.07.0060.
2016
- Frazier TP, Palmer NA, Xie F, Tobias CM, Donze-Reiner T, Bombarely A, Childs K, Shu S, Jenkins J, Schmutz J, Zhang B, Sarath G, Zhao B* (2016) Identification, Characterization, and Gene Expression Analysis of Nucleotide Binding Site (NB)-Type Resistance Gene Homologues in Switchgrass. BMC Genomics 17 (1): 892. doi:10.1186/s12864-016-3201-5.
- Coate J, Song M, Bombarely A, Doyle JJ* (2016) Expression-level support for gene dosage sensitivity in three Glycine subgenus Glycine polyploids and their diploid progenitors. New Phytologist 212 (4), 1083-1093. doi:10.1111/nph.14090.
- Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma M, 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 JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler K, Robbins TP, Schatz MC, Schranz E, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus SL, Vandenbusschen M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C* (2016) Whole genome sequences of the wild parents of the garden petunia give insights into the evolution of Solanaceae genomes. Nature Plants 2: 16074 doi:10.1038/nplants.2016.74.
2015
- Castro JC, Maddox JD, Cobos M, Requena D, Zimic M, Bombarely A, Imán SA, Cerdeira LA, Medina AE* (2015) De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. BMC Genomics 16 (1): 997. doi: 1186/s12864-015-2225-6
- Vallarino JG, Osorio S, Bombarely A, Casañal A, Cruz‐Rus E, Sánchez‐Sevilla JF, Amaya I, Giavalisco P, Fernie AR, Botella MA, Valpuesta V* (2015) Central role of FaGAMYB in the transition of the strawberry receptacle from development to ripening. New Phytologist 208 (2):482-496. doi:10.1111/nph.13463.
- Soliman SSM, Greenwood JS, Bombarely A, Mueller LA, Tsao R, Mosser DD, Raizada MN* (2015) An Endophyte Constructs Fungicide-Containing Extracellular Barriers for Its Host Plant. Current Biology. 25 (19):2570-2576. doi:10.1016/j.cub.2015.08.027.
- Duran I, Csukasi F, Taylor SP, Krakow D, Becerra J, Bombarely A, Marí-Beffa M* (2015) Collagen duplicate genes of bone and cartilage participate during regeneration of zebrafish fin skeleton. Gene Expression Patterns 19 (1): 60-69 doi:10.1016/j.gep.2015.07.004.
- Strickler SR, Bombarely A, Munkvold JD, Menda N, Martin GB, Mueller LA* (2015) Comparative genomics and phylogenetic discordance of cultivated tomato and its nearest wild relatives. 3, e793. doi:10.7717/peerj.793.
- Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA* (2015) The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. Nucleic Acids Research. 43 (D1), D1036-D1041; doi: 10.1093/nar/gku1195
2014
- Kang YJ , Kim S, Kim MY , Lestari P, Kim KH, Ha BK, Jun TH, Hwang WJ, Lee T, Lee J, Shim S, Yoon MY, Jang YE, Han KS, Taeprayoon P, Yoon N, Somta P, Tanya P, Kim KS, Gwag JG, Moon JK, Lee YH, Park BS, Bombarely A, Doyle J, Jackson S, Schafleitner R, Srinives P, Varshney R* (2014) Genome sequence of mungbean and insights into evolution within Vigna species. Nature Communications. 5: 5443 doi:10.1038/ncomms6443.
- Menda N, Stricker SR, Edwards JD, Bombarely A, Dunham DM, Martin GB, Mejia L, Hutton SF, Havey MJ, Maxwell DP, Mueller LA*. (2014) Analysis of introgressions in the genome of a begomovirus-resistant tomato inbred uncovers origins of its wild ancestors. BMC Plant Biology 14 (1): 287. doi:10.1186/s12870-014-0287-2.
- Sherman-Broyles S, Bombarely A, Powell AF, Doyle JL, Egan AN, Coate JE, Doyle JJ* (2014) The wild side of a major crop: Soybean’s perennial cousins from Down Under. American Journal of Botany 101:1651-1665. doi:10.3732/ajb.1400121.
- Sherman-Broyles S, Bombarely A, Grimwood J, Schmutz J, Doyle JJ* (2014) Complete Plastome Sequences from Glycine syndetika, and Six Additional Perennial Wild Relatives of Soybean. G3: Genes| Genomes| Genetics, g3. 114.012690. doi:10.1534/g3.114.012690.
- Bombarely A, Coate JE, Doyle JJ (2014) Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ 2, e391. doi: 7717/peerj.391.
- Villarino GH, Bombarely A, Giovannoni JJ, Scanlon MJ, Mattson NS* (2014) Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing. PloS One 9 (4), e94651. doi:10.1371/journal.pone.0099146.
- Jung S, Ficklin S, Lee T, Cheng CH, Blenda A, Zheng P, Yu J, Bombarely A, Cho, IH, Yu S, Evans K, Peace C, Abbott A, Mueller LA, Olmstead M, Main D*. (2014) The Genome Database for Rosaceae (GDR): Year 10 Update. Nucleic Acid Research 42 (D1), D1237-D1244. doi:10.1093/nar/gkt1012
2013
- Rosli HG, Zheng Y, Pombo MA, Zhong S, Bombarely A, Fei Z, Collmer A, Martin GB* (2013) Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity. Genome Biology 14 (12): R139. doi:10.1186/gb-2013-14-12-r139.
- D’Agostino N, Golas T, van der Geest H, Bombarely A, Dawood T, Zethof J, Driedonks N, Wijnker E, Bargsten J, Nap JP, Mariani C, Rieu I* (2013) Genomic analysis of the native European Solanum species, dulcamara. BMC Genomics 14: 356. doi:10.1186/1471-2164-14-356.
- Pujar A, Menda N, Bombarely A, Edwards JD, Strickler SR, Mueller LA* (2013) From manual curation to visualization of the gene families and networks across the Solanaceae plant species. Database: The Journal of Biological Databases and Curation 2013, bat028. doi: 1093/database/bat028.
- Doblas VG, Amorim-Silva V, Pose D, Rosado A, Esteban A, Arro M, Azevedo H, Bombarely A, Borsani O, Valpuesta V, Ferrer A, Tavares RM, Botella MA* (2013) The Arabidopsis SUD1 Gene, encoding a putative E3 Ubiquitin Ligase, is a Positive Regulator of the 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase Activity. The Plant Cell. 25: 728-743. doi:10.1105/tpc.112.108696.
2012
- Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, Zheng Y, Mao L, Ren Y, Wang Z, Min J, Guo X, Murat F, Ham BK, Zhang Z, Gao S, Huang M, Xu Y, Zhong S, Bombarely A, Mueller LA, 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 JJ, Wang J, Li Y, Fei Z, Xu Y* (2012) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics 45(1): 51-58. doi:10.1038/ng.2470.
- Bombarely A, Edwards KD, Sanchez-Tamburino J, Mueller LA* (2012) Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: A phylogenomic perspective. BMC Genomics 13(1): 187. doi:10.1186/1471-2164-13-406.
- Bombarely A, Rosli HG, Vrebalov J, Moffet P, Mueller LA, Martin GB* (2012) A Draft Genome Sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Molecular Plant-Microbe Interactions. 25(12): 1523-1530. doi:10.1094/MPMI-06-12-0148-TA.
- Tomato Sequencing Consortium (2012), The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485 (7400): 635-641. doi:10.1038/nature11119.
- Lima-Silva V, Rosado A, Amorin-Silva V, Muñoz-Mérida A, Pons C, Bombarely A, Trelles O, Fernández-Muñoz R, Granell A, Valpuesta V, Botella MA* (2012) Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin c content in tomato fruit. BMC Genomics 13 (1), 187. doi:10.1186/1471-2164-13-187.
- Strickler SR, Bombarely A, Mueller LA*. (2012) Designing a Transcriptome Next-Generation Sequencing Project for a Non-model Plant Species. American Journal of Botany 99 (2): 257-266. doi:10.3732/ajb.1100292.
2011
- Osorio S, Bombarely A, Giavalisco P, Usadel B, Stephens C, Aragüez I, Medina-Escobar N, Botella MA, Fernie AR, Valpuesta V* (2011) Demethylation of oligogalacturonides by FaPE1 in the fruits of the wild strawberry Fragaria vesca triggers metabolic and transcriptional changes associated with defence and development of the fruit. Journal of Experimental Botany. 62 (8): 2855. doi:10.1093/jxb/erq465.
- Privat I, Bardil A, Gomez AB, Severac D, Dantec C, Fuentes I, Mueller L, Joët T, Pot D, Foucrier S, Dussert S, Leroy T, Journot L, de Kochko A, Campa C, Combes MC, Lashermes P, Bertrand B*. (2011) The ‘PUCE CAFE’ Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits. BMC Genomics, 12:5. doi:10.1186/1471-2164-12-5.
- Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA* (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl Nucleic Acids Research 39:D1149-D1155. doi:10.1093/nar/gkq866.
2010
- Bombarely A, Merchante C, Csukasi F, Cruz-Rus E, Caballero JL, Medina-Escobar N, Blanco-Portales R, Botella MA, Muñoz-Blanco J, Sánchez-Sevilla JF, Valpuesta V* (2010) Generation and analysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies. BMC Genomics, 11:503. doi:10.1186/1471-2164-11-503.
- Edwards KD, Bombarely A, Story GW, Allen F, Mueller LA, Coates SA, Jones L* (2010) TobEA: an atlas of tobacco gene expression from seed to senescence BMC Genomics, 11:142. doi:10.1186/1471-2164-11-142.
2009
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