Claros, M. G., Bullones, A., Castro, A. J., Lima-Cabello, E., Viruel, M. Á., Suárez, M. F., Romero-Aranda, R., Fernández-Pozo, N., Veredas, F. J., Belver, A., & Alché, J. de D. (2025). Multi-Omic Advances in Olive Tree (Olea europaea subsp. europaea L.) Under Salinity: Stepping Towards ‘Smart Oliviculture.’ Biology, 14(3), 287. https://doi.org/10.3390/biology14030287

Mérai, Z., Graeber, K., Xu, F., Dona, M., Lalatović, K., Wilhelmsson, P. K. I., Fernandez-Pozo, N., Rensing, S. A., Leubner-Metzger, G., Scheid, O. M., & Dolan, L. (2024). Long days induce adaptive secondary dormancy in seed of the Mediterranean plantAethionema arabicum. https://doi.org/10.1101/2024.01.08.574645

Chandler, J. O., Wilhelmsson, P. K. I., Fernandez-Pozo, N., Graeber, K., Arshad, W., Pérez, M., Steinbrecher, T., Ullrich, K. K., Nguyen, T.-P., Mérai, Z., Mummenhoff, K., Theißen, G., Strnad, M., Mittelsten Scheid, O., Schranz, M. E., Petřík, I., Tarkowská, D., Novák, O., Rensing, S. A., & Leubner-Metzger, G. (2024). The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures. The Plant Cell, 36(7), 2465–2490. https://doi.org/10.1093/plcell/koae085

Claros, M. G., Bullones, A., Castro, A. J., Lima-Cabello, E., Viruel, M. Á., Suárez, M. F., Romero-Aranda, M. R., Fernández-Pozo, N., Veredas, F. J., Belver, A., & Alché, J. de D. (2024). Genomics Advances in olive tree (<i>Olea europaea</i> subsp. <i>europaea</i> L.) to Mitigate the Effects of Soil Salinisation: Stepping Towards the “Smart Oliviculture.” https://doi.org/10.20944/preprints202411.2291.v1

Fernandez-Pozo, N. (2023). PEATmoss: A Gene Expression Atlas for Bryophytes. Plant Genomic and Cytogenetic Databases, 91–107. https://doi.org/10.1007/978-1-0716-3389-2_8

Bullones, A., Castro, A. J., Lima-Cabello, E., Alché, J. de D., Luque, F., Claros, M. G., & Fernandez-Pozo, N. (2023). OliveAtlas: A Gene Expression Atlas Tool for Olea europaea. Plants, 12(6), 1274. https://doi.org/10.3390/plants12061274

Gómez-Ollé, A., Bullones, A., Hormaza, J. I., Mueller, L. A., & Fernandez-Pozo, N. (2023). MangoBase: A Genomics Portal and Gene Expression Atlas for Mangifera indica. Plants, 12(6), 1273. https://doi.org/10.3390/plants12061273

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

Bullones, A., Castro, A. J., Lima-Cabello, E., Fernandez-Pozo, N., Bautista, R., Alché, J. de D., & Claros, M. G. (2023). Transcriptomic Insight into the Pollen Tube Growth of Olea europaea L. subsp. europaea Reveals Reprogramming and Pollen-Specific Genes Including New Transcription Factors. Plants, 12(16), 2894. https://doi.org/10.3390/plants12162894

Ontiveros, I., Fernández-Pozo, N., Esteve-Codina, A., López-Moya, J. J., & Díaz-Pendón, J. A. (2023). Enhanced Susceptibility to Tomato Chlorosis Virus (ToCV) in <em>Hsp90</em> and <em>Sgt1</em> Silenced Plants: Insights from Gene Expression Dynamics. https://doi.org/10.20944/preprints202311.0162.v1

Murik, O., Geffen, O., Shotland, Y., Fernandez‐Pozo, N., Ullrich, K. K., Walther, D., Rensing, S. A., & Treves, H. (2023). Genomic imprints of unparalleled growth. New Phytologist, 241(3), 1144–1160. Portico. https://doi.org/10.1111/nph.19444

Fernandez-Pozo, N., Haas, F. B., Gould, S. B., & Rensing, S. A. (2022). An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes. Journal of Experimental Botany, 73(13), 4291–4305. https://doi.org/10.1093/jxb/erac052

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

Gramzow, L., Klupsch, K., Fernández-Pozo, N., Hölzer, M., Marz, M., Rensing, S. A., & Theißen, G. (2022). Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae). BMC Plant Biology, 22(1). https://doi.org/10.1186/s12870-022-03631-8

Fernandez‐Pozo, N., Metz, T., Chandler, J. O., Gramzow, L., Mérai, Z., Maumus, F., Mittelsten Scheid, O., Theißen, G., Schranz, M. E., Leubner‐Metzger, G., & Rensing, S. A. (2021). Aethionema arabicum genome annotation using PacBio full‐length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. The Plant Journal, 106(1), 275–293. Portico. https://doi.org/10.1111/tpj.15161

Can, S. N., Nunn, A., Galanti, D., Langenberger, D., Becker, C., Volmer, K., Heer, K., Opgenoorth, L., Fernandez-Pozo, N., & Rensing, S. A. (2021). The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline. Epigenomes, 5(2), 12. https://doi.org/10.3390/epigenomes5020012

Genau, A. C., Li, Z., Renzaglia, K. S., Fernandez Pozo, N., Nogué, F., Haas, F. B., Wilhelmsson, P. K. I., Ullrich, K. K., Schreiber, M., Meyberg, R., Grosche, C., & Rensing, S. A. (2021). HAG1 and SWI3A/B control of male germ line development in P. patens suggests conservation of epigenetic reproductive control across land plants. Plant Reproduction, 34(2), 149–173. https://doi.org/10.1007/s00497-021-00409-0

Carey, S. B., Jenkins, J., Lovell, J. T., Maumus, F., Sreedasyam, A., Payton, A. C., Shu, S., Tiley, G. P., Fernandez-Pozo, N., Healey, A., Barry, K., Chen, C., Wang, M., Lipzen, A., Daum, C., Saski, C. A., McBreen, J. C., Conrad, R. E., Kollar, L. M., … McDaniel, S. F. (2021). Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. Science Advances, 7(27). https://doi.org/10.1126/sciadv.abh2488

Nunn, A., Can, S. N., Otto, C., Fasold, M., Díez Rodríguez, B., Fernández-Pozo, N., Rensing, S. A., Stadler, P. F., & Langenberger, D. (2021). EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics. NAR Genomics and Bioinformatics, 3(4). https://doi.org/10.1093/nargab/lqab106

Gramzow, L., Klupsch, K., Fernández Pozo, N., Hölzer, M., Marz, M., Rensing, S. A., & Theißen, G. (2021). Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae). https://doi.org/10.1101/2021.10.29.466389

Pombo, M. A., Rosli, H. G., Fernandez-Pozo, N., & Bombarely, A. (2020). Nicotiana benthamiana, A Popular Model for Genome Evolution and Plant–Pathogen Interactions. The Tobacco Plant Genome, 231–247. https://doi.org/10.1007/978-3-030-29493-9_14

Li, F.-W., Nishiyama, T., Waller, M., Frangedakis, E., Keller, J., Li, Z., Fernandez-Pozo, N., Barker, M. S., Bennett, T., Blázquez, M. A., Cheng, S., Cuming, A. C., de Vries, J., de Vries, S., Delaux, P.-M., Diop, I. S., Harrison, C. J., Hauser, D., Hernández-García, J., … Szövényi, P. (2020). Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nature Plants, 6(3), 259–272. https://doi.org/10.1038/s41477-020-0618-2

Kreutz, C., Can, N. S., Bruening, R. S., Meyberg, R., Mérai, Z., Fernandez-Pozo, N., & Rensing, S. A. (2020). A blind and independent benchmark study for detecting differentially methylated regions in plants. Bioinformatics, 36(11), 3314–3321. https://doi.org/10.1093/bioinformatics/btaa191

Jiménez‐Ruiz, J., Ramírez‐Tejero, J. A., Fernández‐Pozo, N., Leyva‐Pérez, M. de la O., Yan, H., Rosa, R. de la, Belaj, A., Montes, E., Rodríguez‐Ariza, M. O., Navarro, F., Barroso, J. B., Beuzón, C. R., Valpuesta, V., Bombarely, A., & Luque, F. (2020). Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.). The Plant Genome, 13(1). Portico. https://doi.org/10.1002/tpg2.20010

Fernandez‐Pozo, N., Haas, F. B., Meyberg, R., Ullrich, K. K., Hiss, M., Perroud, P., 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, L. A., & Rensing, S. A. (2020). PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. The Plant Journal, 102(1), 165–177. Portico. https://doi.org/10.1111/tpj.14607

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, J. J., Mueller, L. A., Slupsky, C. M., Bruce, J. E., & Heck, M. (2020). Longitudinal Transcriptomic, Proteomic, and Metabolomic Analysis of Citrus limon Response to Graft Inoculation by Candidatus Liberibacter asiaticus. Journal of Proteome Research, 19(6), 2247–2263. https://doi.org/10.1021/acs.jproteome.9b00802

Sun, G., Bai, S., Guan, Y., Wang, S., Wang, Q., Liu, Y., Liu, H., Goffinet, B., Zhou, Y., Paoletti, M., Hu, X., Haas, F. B., Fernandez‐Pozo, N., Czyrt, A., Sun, H., Rensing, S. A., & Huang, J. (2020). Are fungi‐derived genomic regions related to antagonism towards fungi in mosses? New Phytologist, 228(4), 1169–1175. Portico. https://doi.org/10.1111/nph.16776

Carey, S. B., Jenkins, J., Lovell, J. T., Maumus, F., Sreedasyam, A., Payton, A. C., Shu, S., Tiley, G. P., Fernandez-Pozo, N., Barry, K., Chen, C., Wang, M., Lipzen, A., Daum, C., Saski, C. A., McBreen, J. C., Conrad, R. E., Kollar, L. M., Olsson, S., … McDaniel, S. F. (2020). The Ceratodon purpureus genome uncovers structurally complex, gene rich sex chromosomes. https://doi.org/10.1101/2020.07.03.163634

Haas, F. B., Fernandez-Pozo, N., Meyberg, R., Perroud, P.-F., Göttig, M., Stingl, N., Saint-Marcoux, D., Langdale, J. A., & Rensing, S. A. (2020). Single Nucleotide Polymorphism Charting of P. patens Reveals Accumulation of Somatic Mutations During in vitro Culture on the Scale of Natural Variation by Selfing. Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.00813

Treves, H., Siemiatkowska, B., Luzarowska, U., Murik, O., Fernandez-Pozo, N., Moraes, T. A., Erban, A., Armbruster, U., Brotman, Y., Kopka, J., Rensing, S. A., Szymanski, J., & Stitt, M. (2020). Multi-omics reveals mechanisms of total resistance to extreme illumination of a desert alga. Nature Plants, 6(8), 1031–1043. https://doi.org/10.1038/s41477-020-0729-9

Wilhelmsson, P. K. I., Chandler, J. O., Fernandez-Pozo, N., Graeber, K., Ullrich, K. K., Arshad, W., Khan, S., Hofberger, J. A., Buchta, K., Edger, P. P., Pires, J. C., Schranz, M. E., Leubner-Metzger, G., & Rensing, S. A. (2019). Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-019-5452-4

Flores-Gonzalez, M., Hosmani, P. S., Fernandez-Pozo, N., Mann, M., Humann, J. L., Main, D., Heck, M., Brown, S., Mueller, L. A., & Saha, S. (2019). Citrusgreening.org: An open access and integrated systems biology portal for the Huanglongbing (HLB) disease complex. https://doi.org/10.1101/868364

Shinozaki, Y., Nicolas, P., Fernandez-Pozo, N., Ma, Q., Evanich, D. J., Shi, Y., Xu, Y., Zheng, Y., Snyder, S. I., Martin, L. B. B., Ruiz-May, E., Thannhauser, T. W., Chen, K., Domozych, D. S., Catalá, C., Fei, Z., Mueller, L. A., Giovannoni, J. J., & Rose, J. K. C. (2018). High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nature Communications, 9(1). https://doi.org/10.1038/s41467-017-02782-9

Schwizer, S., Kraus, C. M., Dunham, D. M., Zheng, Y., Fernandez-Pozo, N., Pombo, M. A., Fei, Z., Chakravarthy, S., & Martin, G. B. (2017). The Tomato Kinase Pti1 Contributes to Production of Reactive Oxygen Species in Response to Two Flagellin-Derived Peptides and Promotes Resistance to Pseudomonas syringae Infection. Molecular Plant-Microbe Interactions®, 30(9), 725–738. https://doi.org/10.1094/mpmi-03-17-0056-r

Fernandez-Pozo, N., Zheng, Y., Snyder, S. I., Nicolas, P., Shinozaki, Y., Fei, Z., Catala, C., Giovannoni, J. J., Rose, J. K. C., & Mueller, L. A. (2017). The Tomato Expression Atlas. Bioinformatics, 33(15), 2397–2398. https://doi.org/10.1093/bioinformatics/btx190

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

Mueller, L., & Fernandez-Pozo, N. (2016). Tomato Databases. The Tomato Genome, 245–255. https://doi.org/10.1007/978-3-662-53389-5_13

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

Seoane-Zonjic, P., Cañas, R. A., Bautista, R., Gómez-Maldonado, J., Arrillaga, I., Fernández-Pozo, N., Claros, M. G., Cánovas, F. M., & Ávila, C. (2016). Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing. BMC Genomics, 17(1). https://doi.org/10.1186/s12864-016-2490-z

Osorio-Guarín, J. A., Enciso-Rodríguez, F. E., González, C., Fernández-Pozo, N., Mueller, L. A., & Barrero, L. S. (2016). Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L). BMC Genomics, 17(1). https://doi.org/10.1186/s12864-016-2568-7

Fernandez-Pozo, N., Rosli, H. G., Martin, G. B., & Mueller, L. A. (2015). The SGN VIGS Tool: User-Friendly Software to Design Virus-Induced Gene Silencing (VIGS) Constructs for Functional Genomics. Molecular Plant, 8(3), 486–488. https://doi.org/10.1016/j.molp.2014.11.024

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, L. A., & Jander, G. (2015). Dynamic maize responses to aphid feeding are revealed by a time series of transcriptomic and metabolomic assays. Plant Physiology, pp.01039.2015. https://doi.org/10.1104/pp.15.01039

Pombo, M. A., Zheng, Y., Fernandez-Pozo, N., Dunham, D. M., Fei, Z., & Martin, G. B. (2014). Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins. Genome Biology, 15(10). https://doi.org/10.1186/s13059-014-0492-1

Singh, D. K., Calviño, M., Brauer, E. K., Fernandez-Pozo, N., Strickler, S., Yalamanchili, R., Suzuki, H., Aoki, K., Shibata, D., Stratmann, J. W., Popescu, G. V., Mueller, L. A., & Popescu, S. C. (2014). The Tomato Kinome and the Tomato Kinase Library ORFeome: Novel Resources for the Study of Kinases and Signal Transduction in Tomato and Solanaceae Species. Molecular Plant-Microbe Interactions®, 27(1), 7–17. https://doi.org/10.1094/mpmi-08-13-0218-ta

Benzekri, H., Armesto, P., Cousin, X., Rovira, M., Crespo, D., Merlo, M. A., Mazurais, D., Bautista, R., Guerrero-Fernández, D., Fernandez-Pozo, N., Ponce, M., Infante, C., Zambonino, J. L., Nidelet, S., Gut, M., Rebordinos, L., Planas, J. V., Bégout, M.-L., Claros, M. G., & Manchado, M. (2014). De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-952

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

Benzekri, H., Bautista, R., Guerrero-Fernández, D., Fernández-Pozo, N., & Claros, M. G. (2013). A reliable pipeline for a transcriptome reference in Non-Model Species. EMBnet.Journal, 19(A), 38. https://doi.org/10.14806/ej.19.a.611

Canales, J., Bautista, R., Label, P., Gómez‐Maldonado, J., Lesur, I., Fernández‐Pozo, N., Rueda‐López, M., Guerrero‐Fernández, D., Castro‐Rodríguez, V., Benzekri, H., Cañas, R. A., Guevara, M., Rodrigues, A., Seoane, P., Teyssier, C., Morel, A., Ehrenmann, F., Le Provost, G., Lalanne, C., … Cánovas, F. M. (2013). De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotechnology Journal, 12(3), 286–299. Portico. https://doi.org/10.1111/pbi.12136

Claros, M. G., Bautista, R., Guerrero-Fernández, D., Benzerki, H., Seoane, P., & Fernández-Pozo, N. (2012). Why Assembling Plant Genome Sequences Is So Challenging. Biology, 1(2), 439–459. https://doi.org/10.3390/biology1020439

Fernández-Pozo, N., Guerrero-Fernández, D., Bautista, R., Gómez-Maldonado, J., Avila, C., Cánovas, F. M., & Claros, M. G. (2012). GENote v.β: A Web Tool Prototype for Annotation of Unfinished Sequences in Non-model Eukaryotes. Bioinformatics for Personalized Medicine, 66–71. https://doi.org/10.1007/978-3-642-28062-7_7

Fernández-Pozo, N., Canales, J., Guerrero-Fernández, D., Villalobos, D. P., Díaz-Moreno, S. M., Bautista, R., Flores-Monterroso, A., Guevara, M. Á., Perdiguero, P., Collada, C., Cervera, M. T., Soto, Á., Ordás, R., Cantón, F. R., Avila, C., Cánovas, F. M., & Claros, M. G. (2011). EuroPineDB: a high-coverage web database for maritime pine transcriptome. BMC Genomics, 12(1). https://doi.org/10.1186/1471-2164-12-366

Sanz-Santos, G., Jiménez-Marín, Á., Bautista, R., Fernández, N., Claros, G. M., & Garrido, J. J. (2011). Gene expression pattern in swine neutrophils after lipopolysaccharide exposure: a time course comparison. BMC Proceedings, 5(S4). https://doi.org/10.1186/1753-6561-5-s4-s11

Falgueras, J., Lara, A. J., Fernández-Pozo, N., Cantón, F. R., Pérez-Trabado, G., & Claros, M. G. (2010). SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinformatics, 11(1). https://doi.org/10.1186/1471-2105-11-38

Falgueras, J., Lara, A. J., Trabado, G. P., Pozo, N. F., Canton, F. R., & Claros, M. G. (2010). SeqTrim07: a pipeline for preprocessing sequence reads. International Journal of Computational Intelligence in Bioinformatics and Systems Biology, 1(4), 370. https://doi.org/10.1504/ijcibsb.2010.038217