Valverde, S., Vidiella, B., Martínez-Redondo, G. I., Duran-Nebreda, S., Fernández, R., Bombarely, A., Rojas, A. M., & Bentley, R. A. (2025). Structural Changes in Gene Ontology Reveal Modular and Complex Representations of Biological Function. Molecular Biology and Evolution, 42(6). https://doi.org/10.1093/molbev/msaf148

Baraja-Fonseca, V., Arrones, A., Vilanova, S., Plazas, M., Prohens, J., Bombarely, A., & Gramazio, P. (2024). Benchmarking of Low Coverage Sequencing Workflows for Precision Genotyping in Eggplant. https://doi.org/10.1101/2024.10.24.619843

Soares, L. S., Bombarely, A., & Freitas, L. B. (2024). How many species are there? Lineage diversification and hidden speciation in Solanaceae from highland grasslands in southern South America. Annals of Botany, 134(7), 1291–1305. https://doi.org/10.1093/aob/mcae144

Talavera, A., Soorni, A., Bombarely, A., Matas, A. J., & Hormaza, J. I. (2023). Author Correction: Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.). Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-29346-w

D’Andrea, L., Perez de Souza, L., Fernie, A. R., & Bombarely, A. (2023). MetPlast: an R package to evaluate Metabolic Plasticity using Information Theory statistical framework. https://doi.org/10.1101/2023.04.28.472208

Gomez, S. K., Maurya, A. K., Irvin, L., Kelly, M. P., Schoenherr, A. P., Huguet-Tapia, J. C., & Bombarely, A. (2023). A snapshot of the transcriptome ofMedicago truncatula(Fabales: Fabaceae) shoots and roots in response to an arbuscular mycorrhizal fungus and the pea aphid (Acyrthosiphon pisum) (Hemiptera: Aphididae). Environmental Entomology, 52(4), 667–680. https://doi.org/10.1093/ee/nvad070

Manrique, S., Cavalleri, A., Guazzotti, A., Villarino, G. H., Simonini, S., Bombarely, A., Higashiyama, T., Grossniklaus, U., Mizzotti, C., Pereira, A. M., Coimbra, S., Sankaranarayanan, S., Onelli, E., Masiero, S., Franks, R. G., & Colombo, L. (2023). HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation. Plant Physiology, 194(4), 2117–2135. https://doi.org/10.1093/plphys/kiad629

Talavera, A., Fernandez‐Pozo, N., Matas, A. J., Hormaza, J. I., & Bombarely, A. (2023). Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya (Annona cherimola). PLANTS, PEOPLE, PLANET, 5(3), 408–423. Portico. https://doi.org/10.1002/ppp3.10366

Yan, H., Haak, D. C., Li, S., Huang, L., & Bombarely, A. (2022). Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice. Plant Communications, 3(3), 100270. https://doi.org/10.1016/j.xplc.2021.100270

Fernandez-Pozo, N., & Bombarely, A. (2022). EasyGDB: a low-maintenance and highly customizable system to develop genomics portals. Bioinformatics, 38(16), 4048–4050. https://doi.org/10.1093/bioinformatics/btac412

Cucinotta, M., Cavalleri, A., Guazzotti, A., Astori, C., Manrique, S., Bombarely, A., Oliveto, S., Biffo, S., Weijers, D., Kater, M. M., & Colombo, L. (2021). Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development. Current Biology, 31(4), 892-899.e3. https://doi.org/10.1016/j.cub.2020.11.026

Garzón-Martínez, G. A., García-Arias, F. L., Enciso-Rodríguez, F. E., Soto-Suárez, M., González, C., Bombarely, A., Barrero, L. S., & Osorio Guarín, J. A. (2021). Combining transcriptome analysis and GWAS for identification and validation of marker genes in thePhysalis peruviana-Fusarium oxysporumpathosystem. PeerJ, 9, e11135. Portico. https://doi.org/10.7717/peerj.11135

Bombarely, A., Doulis, A. G., Lambrou, K. K., 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

Friel, J., Bombarely, A., Fornell, C. D., Luque, F., & Fernández-Ocaña, A. M. (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

Yan, H., Torchiana, F., & Bombarely, A. (2020). Guideline for genome transposon annotation derived from evaluation of popular TE identification tools. https://doi.org/10.20944/preprints202008.0275.v1

Caballero-Villalobos, L., Silva-Arias, G. A., Turchetto, C., Giudicelli, G. C., Petzold, E., Bombarely, A., & Freitas, L. B. (2020). Neutral and adaptive genomic variation in hybrid zones of two ecologically divergedPetuniaspecies (Solanaceae). Botanical Journal of the Linnean Society, 196(1), 100–122. https://doi.org/10.1093/botlinnean/boaa091

Hu, Y., Resende, M. F. R., Bombarely, A., Brym, M., Bassil, E., & Chambers, A. H. (2019). Genomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencing. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-40144-1

Manrique, S., Friel, J., Gramazio, P., Hasing, T., Ezquer, I., & Bombarely, A. (2019). Genetic insights into 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

Soorni, A., Borna, T., Alemardan, A., Chakrabarti, M., Hunt, A. G., & Bombarely, A. (2019). Transcriptome Landscape Variation in the Genus Thymus. Genes, 10(8), 620. https://doi.org/10.3390/genes10080620

Hasing, T., Rinaldi, E., Manrique, S., Colombo, L., Haak, D. C., 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(4), 363–374. Portico. https://doi.org/10.1002/ppp3.10065

Talavera, A., Soorni, A., Bombarely, A., Matas, A. J., & Hormaza, J. I. (2019). Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.). Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-56526-4

Blankers, T., Oh, K. P., Bombarely, A., & Shaw, K. L. (2018). The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian CricketLaupala. Genetics, 209(4), 1329–1344. https://doi.org/10.1534/genetics.118.300894

Zhao, C., Lasses, T., Bako, L., Kong, D., Zhao, B., Chanda, B., Bombarely, A., Cruz‐Ramírez, A., Scheres, B., Brunner, A. M., & Beers, E. P. (2017). XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA‐RELATED. New Phytologist, 216(1), 76–89. Portico. https://doi.org/10.1111/nph.14704

Jiménez‐Ruiz, J., Leyva‐Pérez, M. de la O., Schilirò, E., Barroso, J. B., Bombarely, A., Mueller, L., Mercado‐Blanco, J., & Luque, F. (2017). Transcriptomic Analysis of Olea europaea L. Roots during the Verticillium dahliae Early Infection Process. The Plant Genome, 10(1). Portico. https://doi.org/10.3835/plantgenome2016.07.0060

Mizzotti, C., Galliani, B. M., Dreni, L., Sommer, H., Bombarely, A., & Masiero, S. (2017). ERAMOSA controls lateral branching in snapdragon. Scientific Reports, 7(1). https://doi.org/10.1038/srep41319

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. (2017). De novo assembly of the zucchini genome reveals a whole‐genome duplication associated with the origin of the Cucurbita genus. Plant Biotechnology Journal, 16(6), 1161–1171. Portico. https://doi.org/10.1111/pbi.12860

Sherman‐Broyles, S., Bombarely, A., & Doyle, J. (2017). Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies. Journal of Systematics and Evolution, 55(4), 365–376. Portico. https://doi.org/10.1111/jse.12268

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. (2017). De-novoassembly of zucchini genome reveals a whole genome duplication associated with the origin of theCucurbitagenus. https://doi.org/10.1101/147702

Villarino, G. H., Hu, Q., Scanlon, M. J., Mueller, L., Bombarely, A., & Mattson, N. S. (2017). Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell. Genes, 8(8), 195. https://doi.org/10.3390/genes8080195

Sánchez-Sevilla, J. F., Vallarino, J. G., Osorio, S., Bombarely, A., Posé, D., Merchante, C., Botella, M. A., 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(1). https://doi.org/10.1038/s41598-017-14239-6

Soorni, A., Fatahi, R., Haak, D. C., Salami, S. A., & Bombarely, A. (2017). Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-15816-5

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). https://doi.org/10.1186/s12864-016-3412-9

Carlson, K. D., Fernandez-Pozo, N., Bombarely, A., Pisupati, R., Mueller, L. A., & Madlung, A. (2017). Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica. BMC Genomics, 18(1). https://doi.org/10.1186/s12864-017-4067-x

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, L. A. (2017). A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genomics, 18(1). https://doi.org/10.1186/s12864-017-3791-6

Frazier, T. P., Palmer, N. A., Xie, F., Tobias, C. M., Donze-Reiner, T. J., Bombarely, A., Childs, K. L., Shu, S., Jenkins, J. W., 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). https://doi.org/10.1186/s12864-016-3201-5

Coate, J. E., Song, M. J., Bombarely, A., & Doyle, J. J. (2016). Expression‐level support for gene dosage sensitivity in three Glycine subgenus Glycine polyploids and their diploid progenitors. New Phytologist, 212(4), 1083–1093. Portico. https://doi.org/10.1111/nph.14090

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., … Kuhlemeier, C. (2016). Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants, 2(6). https://doi.org/10.1038/nplants.2016.74

Castro, J. C., Maddox, J. D., Cobos, M., Requena, D., Zimic, M., Bombarely, A., Imán, S. A., Cerdeira, L. A., & Medina, A. E. (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). https://doi.org/10.1186/s12864-015-2225-6

Strickler, S. R., Bombarely, A., Munkvold, J. D., York, T., Menda, N., Martin, G. B., & Mueller, L. A. (2015). Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives. PeerJ, 3, e793. https://doi.org/10.7717/peerj.793

Duran, I., Csukasi, F., Taylor, S. P., 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(1–2), 60–69. https://doi.org/10.1016/j.gep.2015.07.004

Vallarino, J. G., Osorio, S., Bombarely, A., Casañal, A., Cruz‐Rus, E., Sánchez‐Sevilla, J. F., Amaya, I., Giavalisco, P., Fernie, A. R., Botella, M. A., & Valpuesta, V. (2015). Central role of FaGAMYB in the transition of the strawberry receptacle from development to ripening. New Phytologist, 208(2), 482–496. Portico. https://doi.org/10.1111/nph.13463

Soliman, S. S. M., Greenwood, J. S., Bombarely, A., Mueller, L. A., Tsao, R., Mosser, D. D., & Raizada, M. N. (2015). An Endophyte Constructs Fungicide-Containing Extracellular Barriers for Its Host Plant. Current Biology, 25(19), 2570–2576. https://doi.org/10.1016/j.cub.2015.08.027

Villarino, G. H., Bombarely, A., Giovannoni, J. J., Scanlon, M. J., & Mattson, N. S. (2014). Transcriptomic Analysis of Petunia hybrida in Response to Salt Stress Using High Throughput RNA Sequencing. PLoS ONE, 9(4), e94651. https://doi.org/10.1371/journal.pone.0094651

Sherman‐Broyles, S., Bombarely, A., Powell, A. F., Doyle, J. L., Egan, A. N., Coate, J. E., & Doyle, J. J. (2014). The wild side of a major crop: Soybean’s perennial cousins from Down Under. American Journal of Botany, 101(10), 1651–1665. Portico. https://doi.org/10.3732/ajb.1400121

Bombarely, A., Coate, J. E., & Doyle, J. J. (2014). Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ, 2, e391. https://doi.org/10.7717/peerj.391

Kang, Y. J., Kim, S. K., Kim, M. Y., Lestari, P., Kim, K. H., Ha, B.-K., Jun, T. H., Hwang, W. J., Lee, T., Lee, J., Shim, S., Yoon, M. Y., Jang, Y. E., Han, K. S., Taeprayoon, P., Yoon, N., Somta, P., Tanya, P., Kim, K. S., … Lee, S.-H. (2014). Genome sequence of mungbean and insights into evolution within Vigna species. Nature Communications, 5(1). https://doi.org/10.1038/ncomms6443

Sherman-Broyles, S., Bombarely, A., Grimwood, J., Schmutz, J., & Doyle, J. (2014). Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean. G3 Genes|Genomes|Genetics, 4(10), 2023–2033. https://doi.org/10.1534/g3.114.012690

Menda, N., Strickler, S. R., Edwards, J. D., Bombarely, A., Dunham, D. M., Martin, G. B., Mejia, L., Hutton, S. F., Havey, M. J., Maxwell, D. P., & Mueller, L. A. (2014). Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. BMC Plant Biology, 14(1). https://doi.org/10.1186/s12870-014-0287-2

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, L. A. (2014). The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. Nucleic Acids Research, 43(D1), D1036–D1041. https://doi.org/10.1093/nar/gku1195

Rosli, H. G., Zheng, Y., Pombo, M. A., Zhong, S., Bombarely, A., Fei, Z., Collmer, A., & Martin, G. B. (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). https://doi.org/10.1186/gb-2013-14-12-r139

Doblas, V. G., Amorim-Silva, V., Posé, D., Rosado, A., Esteban, A., Arró, M., Azevedo, H., Bombarely, A., Borsani, O., Valpuesta, V., Ferrer, A., Tavares, R. M., & Botella, M. A. (2013). TheSUD1Gene Encodes a Putative E3 Ubiquitin Ligase and Is a Positive Regulator of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase Activity inArabidopsis   . The Plant Cell, 25(2), 728–743. https://doi.org/10.1105/tpc.112.108696

D’Agostino, N., Golas, T., van de Geest, H., Bombarely, A., Dawood, T., Zethof, J., Driedonks, N., Wijnker, E., Bargsten, J., Nap, J.-P., Mariani, C., & Rieu, I. (2013). Genomic analysis of the native European Solanum species, S. dulcamara. BMC Genomics, 14(1). https://doi.org/10.1186/1471-2164-14-356

Pujar, A., Menda, N., Bombarely, A., Edwards, J. D., Strickler, S. R., & Mueller, L. A. (2013). From manual curation to visualization of gene families and networks across Solanaceae plant species. Database, 2013. https://doi.org/10.1093/database/bat028

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, L. A., Olmstead, M. A., & Main, D. (2013). The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Research, 42(D1), D1237–D1244. https://doi.org/10.1093/nar/gkt1012

(2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), 635–641. https://doi.org/10.1038/nature11119

Lima-Silva, V., Rosado, A., Amorim-Silva, V., Muñoz-Mérida, A., Pons, C., Bombarely, A., Trelles, O., Fernández-Muñoz, R., Granell, A., Valpuesta, V., & Botella, M. Á. (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). https://doi.org/10.1186/1471-2164-13-187

Bombarely, A., Edwards, K. D., Sanchez-Tamburrino, J., & Mueller, L. A. (2012). Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective. BMC Genomics, 13(1). https://doi.org/10.1186/1471-2164-13-406

Strickler, S. R., Bombarely, A., & Mueller, L. A. (2012). Designing a transcriptome next‐generation sequencing project for a nonmodel plant species1. American Journal of Botany, 99(2), 257–266. Portico. https://doi.org/10.3732/ajb.1100292

Bombarely, A., Rosli, H. G., Vrebalov, J., Moffett, P., Mueller, L. A., & Martin, G. B. (2012). A Draft Genome Sequence ofNicotiana benthamianato Enhance Molecular Plant-Microbe Biology Research. Molecular Plant-Microbe Interactions®, 25(12), 1523–1530. https://doi.org/10.1094/mpmi-06-12-0148-ta

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., … Xu, Y. (2012). The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics, 45(1), 51–58. https://doi.org/10.1038/ng.2470

Privat, I., Bardil, A., Gomez, A. B., 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, M.-C., 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(1). https://doi.org/10.1186/1471-2164-12-5

Osorio, S., Bombarely, A., Giavalisco, P., Usadel, B., Stephens, C., Aragüez, I., Medina-Escobar, N., Botella, M. A., Fernie, A. R., & 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), 2855–2873. https://doi.org/10.1093/jxb/erq465

Edwards, K. D., Bombarely, A., Story, G. W., Allen, F., Mueller, L. A., Coates, S. A., & Jones, L. (2010). TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics, 11(1), 142. https://doi.org/10.1186/1471-2164-11-142

Bombarely, A., Merchante, C., Csukasi, F., Cruz-Rus, E., Caballero, J. L., Medina-Escobar, N., Blanco-Portales, R., Botella, M. A., Muñoz-Blanco, J., Sánchez-Sevilla, J. F., & 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(1). https://doi.org/10.1186/1471-2164-11-503

Bombarely, A., Menda, N., Tecle, I. Y., Buels, R. M., Strickler, S., Fischer-York, T., Pujar, A., Leto, J., Gosselin, J., & Mueller, L. A. (2010). The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Research, 39(Database), D1149–D1155. https://doi.org/10.1093/nar/gkq866

Mueller, L. A., Lankhorst, R. K., Tanksley, S. D., Giovannoni, J. J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A. A., Menda, N., Tecle, I. Y., Bombarely, A., Stack, S., Royer, S. M., Chang, S., Shearer, L. A., Kim, B. D., Jo, S., … Stiekema, W. (2009). A Snapshot of the Emerging Tomato Genome Sequence. The Plant Genome, 2(1). Portico. https://doi.org/10.3835/plantgenome2008.08.0005

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