Research group

Analysis packages (R, Python, etc.), Bioinformatics education, Bioinformatics Software and Tools, Biological Databases, Cloud Computing, Computational Methods, Computational Techniques, Data Analysis, Data Visualization, Desktop application, Evolutionary modelling, Expression Profiling, FAIRfication, Gene regulatory networks, Genomics, High-performance Computing, Molecular evolution, Non-model organisms, Omics, Parallel Computing, Phylogenetic Analysis, Plant genomics, Population dynamics, RNA Sequencing (RNA-seq), Sequence analysis, Structural bioinformatics, Structure prediction, Transcriptomics

Ksouri, N., Moreno, M. Á., Contreras-Moreira, B., & Gogorcena, Y. (2024). Mapping the genomic landscape of peach and almond with PrunusMap. https://doi.org/10.1101/2024.03.26.586732

Fadón, E., Herrera, S., Gheban, T. I., & Rodrigo, J. (2023). Chilling Requirements of Apricot (Prunus armeniaca L.) Cultivars Using Male Meiosis as a Dormancy Biomarker. Plants, 12(17), 3025. https://doi.org/10.3390/plants12173025

Herrera, S., Lora, J., Hormaza, J. I., & Rodrigo, J. (2022). Self-Incompatibility in Apricot: Identifying Pollination Requirements to Optimize Fruit Production. Plants, 11(15), 2019. https://doi.org/10.3390/plants11152019

Herrera, S., Lora, J., Hormaza, J. I., & Rodrigo, J. (2022). Pollination requirements of new apricot (Prunus armeniaca L.) cultivars. Acta Horticulturae, 1342, 259–268. https://doi.org/10.17660/actahortic.2022.1342.37

Herrera, S., Lora, J., Fadón, E., Hedhly, A., Alonso, J. M., Hormaza, J. I., & Rodrigo, J. (2022). Male Meiosis as a Biomarker for Endo- to Ecodormancy Transition in Apricot. Frontiers in Plant Science, 13. https://doi.org/10.3389/fpls.2022.842333

Beier, S., Fiebig, A., Pommier, C., Liyanage, I., Lange, M., Kersey, P. J., Weise, S., Finkers, R., Koylass, B., Cezard, T., Courtot, M., Contreras-Moreira, B., Naamati, G., Dyer, S., & Scholz, U. (2022). Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR. F1000Research, 11, 231. https://doi.org/10.12688/f1000research.109080.1

Herrera, S., Lora, J., Hormaza, J. I., & Rodrigo, J. (2021). Pollination Management in Stone Fruit Crops. Production Technology of Stone Fruits, 75–102. https://doi.org/10.1007/978-981-15-8920-1_3

Herrera, S., Hormaza, J. I., Lora, J., Ylla, G., & Rodrigo, J. (2021). Molecular Characterization of Genetic Diversity in Apricot Cultivars: Current Situation and Future Perspectives. Agronomy, 11(9), 1714. https://doi.org/10.3390/agronomy11091714

Casas, A. M., Gazulla, C. R., Monteagudo, A., Cantalapiedra, C. P., Moralejo, M., Pilar Gracia, M., Ciudad, F. J., Thomas, W. T. B., Molina-Cano, J. L., Boden, S., Contreras-Moreira, B., & Igartua, E. (2021). Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross. The Crop Journal, 9(4), 862–872. https://doi.org/10.1016/j.cj.2020.07.008

Sancho, R., Inda, L. A., Díaz-Pérez, A., Des Marais, D. L., Gordon, S., Vogel, J., Lusinska, J., Hasterok, R., Contreras-Moreira, B., & Catalán, P. (2021). Tracking the Ancestry of Known and ‘Ghost’ Homeologous Subgenomes in Model Grass Brachypodium Polyploids. https://doi.org/10.1101/2021.05.31.446465

Yates, A. D., Allen, J., Amode, R. M., Azov, A. G., Barba, M., Becerra, A., Bhai, J., Campbell, L. I., Carbajo Martinez, M., Chakiachvili, M., Chougule, K., Christensen, M., Contreras-Moreira, B., Cuzick, A., Da Rin Fioretto, L., Davis, P., De Silva, N. H., Diamantakis, S., Dyer, S., … Flicek, P. (2021). Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research, 50(D1), D996–D1003. https://doi.org/10.1093/nar/gkab1007

Fadón, E., Herrera, S., Guerrero, B., Guerra, M., & Rodrigo, J. (2020). Chilling and Heat Requirements of Temperate Stone Fruit Trees (Prunus sp.). Agronomy, 10(3), 409. https://doi.org/10.3390/agronomy10030409

Herrera, S., Lora, J., Hormaza, J. I., & Rodrigo, J. (2020). Determination of Self- and Inter-(in)compatibility Relationships in Apricot Combining Hand-Pollination, Microscopy and Genetic Analyses. Journal of Visualized Experiments, 160. https://doi.org/10.3791/60241

Fadón, E., Herrera, S., Herrero, M., & Rodrigo, J. (2020). Male meiosis in sweet cherry is constrained by the chilling and forcing phases of dormancy. Tree Physiology, 41(4), 619–630. https://doi.org/10.1093/treephys/tpaa063

Tello-Ruiz, M. K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D., D’Eustachio, P., … Ware, D. (2020). Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research, 49(D1), D1452–D1463. https://doi.org/10.1093/nar/gkaa979

De Silva, N. H., Bhai, J., Chakiachvili, M., Contreras-Moreira, B., Cummins, C., Frankish, A., Gall, A., Genez, T., Howe, K. L., Hunt, S. E., Martin, F. J., Moore, B., Ogeh, D., Parker, A., Parton, A., Ruffier, M., Sakthivel, M. P., Sheppard, D., Tate, J., … Yates, A. D. (2020). The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data. https://doi.org/10.1101/2020.12.18.422865

Herrera, S., Lora, J., Hormaza, J. I., Herrero, M., & Rodrigo, J. (2018). Optimizing Production in the New Generation of Apricot Cultivars: Self-incompatibility, S-RNase Allele Identification, and Incompatibility Group Assignment. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.00527

Herrera, S., Rodrigo, J., Hormaza, J. I., & Lora, J. (2018). Identification of Self-Incompatibility Alleles by Specific PCR Analysis and S-RNase Sequencing in Apricot. International Journal of Molecular Sciences, 19(11), 3612. https://doi.org/10.3390/ijms19113612

Herrera, S., Rodrigo, J., Hormaza, J. I., Herrero, M., & Lora, J. (2018). S-RNaseallele identification and incompatibility group assignment in apricot cultivars. Acta Horticulturae, 1229, 9–14. https://doi.org/10.17660/actahortic.2018.1229.2

Vinuesa, P., Ochoa-Sánchez, L. E., & Contreras-Moreira, B. (2018). GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas. Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.00771

Anda, V. D., Zapata-Peñasco, I., Poot-Hernandez, A. C., Eguiarte, L. E., Contreras-Moreira, B., & Souza, V. (2017). MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. https://doi.org/10.1101/191288

Ito, S., Magalska, A., Alcaraz-Iborra, M., Lopez-Atalaya, J. P., Rovira, V., Contreras-Moreira, B., Lipinski, M., Olivares, R., Martinez-Hernandez, J., Ruszczycki, B., Lujan, R., Geijo-Barrientos, E., Wilczynski, G. M., & Barco, A. (2014). Loss of neuronal 3D chromatin organization causes transcriptional and behavioural deficits related to serotonergic dysfunction. Nature Communications, 5(1). https://doi.org/10.1038/ncomms5450

Serra, T. S., Figueiredo, D. D., Cordeiro, A. M., Almeida, D. M., Lourenço, T., Abreu, I. A., Sebastián, A., Fernandes, L., Contreras-Moreira, B., Oliveira, M. M., & Saibo, N. J. M. (2013). OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors. Plant Molecular Biology, 82(4–5), 439–455. https://doi.org/10.1007/s11103-013-0073-9

Yruela, I., & Contreras-Moreira, B. (2013). Genetic recombination is associated with intrinsic disorder in plant proteomes. BMC Genomics, 14(1), 772. https://doi.org/10.1186/1471-2164-14-772

Contreras-Moreira, B., & Vinuesa, P. (2013). GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis. Applied and Environmental Microbiology, 79(24), 7696–7701. https://doi.org/10.1128/aem.02411-13

Hofmann, K., Silvar, C., Casas, A. M., Herz, M., Büttner, B., Gracia, M. P., Contreras-Moreira, B., Wallwork, H., Igartua, E., & Schweizer, G. (2013). Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces. Theoretical and Applied Genetics, 126(12), 3091–3102. https://doi.org/10.1007/s00122-013-2196-4

Yruela, I., & Contreras-Moreira, B. (2012). Protein disorder in plants: a view from the chloroplast. BMC Plant Biology, 12(1), 165. https://doi.org/10.1186/1471-2229-12-165

Sebastián, Á., P. Cantalapiedra, C., & Contreras-Moreira, B. (2012). Interface Similarity Improves Comparison of DNA-Binding Proteins: The Homeobox Example. Bioinformatics for Personalized Medicine, 72–82. https://doi.org/10.1007/978-3-642-28062-7_8

Sebastian, A., & Contreras-Moreira, B. (2012). The twilight zone of cis element alignments. Nucleic Acids Research, 41(3), 1438–1449. https://doi.org/10.1093/nar/gks1301

Sachman‐Ruiz, B., Contreras‐Moreira, B., Zozaya, E., Martínez‐Garza, C., & Vinuesa, P. (2011). Primers4clades: A Web Server to Design Lineage‐Specific PCR Primers for Gene‐Targeted Metagenomics. Handbook of Molecular Microbial Ecology I, 441–452. Portico. https://doi.org/10.1002/9781118010518.ch51

Casas, A. M., Djemel, A., Ciudad, F. J., Yahiaoui, S., Ponce, L. J., Contreras-Moreira, B., Gracia, M. P., Lasa, J. M., & Igartua, E. (2011). HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys. Theoretical and Applied Genetics, 122(7), 1293–1304. https://doi.org/10.1007/s00122-011-1531-x

Yruela, I., Arilla-Luna, S., Medina, M., & Contreras-Moreira, B. (2010). Evolutionary divergence of chloroplast FAD synthetase proteins. BMC Evolutionary Biology, 10(1), 311. https://doi.org/10.1186/1471-2148-10-311

Janga, S. C., & Contreras-Moreira, B. (2010). Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach. Nucleic Acids Research, 38(20), 6841–6856. https://doi.org/10.1093/nar/gkq612

Contreras-Moreira, B., Sachman-Ruiz, B., Figueroa-Palacios, I., & Vinuesa, P. (2009). primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucleic Acids Research, 37(Web Server), W95–W100. https://doi.org/10.1093/nar/gkp377

Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega-Alvarado, L., Taboada, B., Jimenez-Jacinto, V., Salgado, H., Juárez, K., Contreras-Moreira, B., Huerta, A. M., Collado-Vides, J., & Morett, E. (2009). Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli. PLoS ONE, 4(10), e7526. https://doi.org/10.1371/journal.pone.0007526

Contreras-Moreira, B. (2009). 3D-footprint: a database for the structural analysis of protein–DNA complexes. Nucleic Acids Research, 38(suppl_1), D91–D97. https://doi.org/10.1093/nar/gkp781

Contreras‐Moreira, B., Sancho, J., & Angarica, V. E. (2009). Comparison of DNA binding across protein superfamilies. Proteins: Structure, Function, and Bioinformatics, 78(1), 52–62. Portico. https://doi.org/10.1002/prot.22525

Lozada-Chávez, I., Angarica, V. E., Collado-Vides, J., & Contreras-Moreira, B. (2008). The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks. Journal of Molecular Biology, 379(3), 627–643. https://doi.org/10.1016/j.jmb.2008.04.008

Angarica, V. E., Pérez, A. G., Vasconcelos, A. T., Collado-Vides, J., & Contreras-Moreira, B. (2008). Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics, 9(1). https://doi.org/10.1186/1471-2105-9-436

Vinuesa, P., Rojas-Jiménez, K., Contreras-Moreira, B., Mahna, S. K., Prasad, B. N., Moe, H., Selvaraju, S. B., Thierfelder, H., & Werner, D. (2008). Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of FourBradyrhizobiumSpecies That Nodulate Soybeans on the Asiatic Continent. Applied and Environmental Microbiology, 74(22), 6987–6996. https://doi.org/10.1128/aem.00875-08

Contreras-Moreira, B., Branger, P.-A., & Collado-Vides, J. (2007). TFmodeller: comparative modelling of protein–DNA complexes. Bioinformatics, 23(13), 1694–1696. https://doi.org/10.1093/bioinformatics/btm148

Gama-Castro, S., Jimenez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M. I., Contreras-Moreira, B., Segura-Salazar, J., Muniz-Rascado, L., Martinez-Flores, I., Salgado, H., Bonavides-Martinez, C., Abreu-Goodger, C., Rodriguez-Penagos, C., Miranda-Rios, J., Morett, E., Merino, E., Huerta, A. M., Trevino-Quintanilla, L., & Collado-Vides, J. (2007). RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research, 36(Database), D120–D124. https://doi.org/10.1093/nar/gkm994

Contreras-Moreira, B., & Collado-Vides, J. (2006). Comparative footprinting of DNA-binding proteins. Bioinformatics, 22(14), e74–e80. https://doi.org/10.1093/bioinformatics/btl215

Contreras-Moreira, B., Ezkurdia, I., Tress, M. L., & Valencia, A. (2005). Empirical limits for template‐based protein structure prediction: the CASP5 example. FEBS Letters, 579(5), 1203–1207. Portico. https://doi.org/10.1016/j.febslet.2005.01.014

Smith, G. R., Contreras-Moreira, B., Zhang, X., & Bates, P. A. (2004). A link between sequence conservation and domain motion within the AAA+ family. Journal of Structural Biology, 146(1–2), 189–204. https://doi.org/10.1016/j.jsb.2003.11.022

Contreras-Moreira, B., Jonsson, P. F., & Bates, P. A. (2003). Structural Context of Exons in Protein Domains: Implications for Protein Modelling and Design. Journal of Molecular Biology, 333(5), 1045–1059. https://doi.org/10.1016/j.jmb.2003.09.023

Sellar, G. C., Watt, K. P., Rabiasz, G. J., Stronach, E. A., Li, L., Miller, E. P., Massie, C. E., Miller, J., Contreras-Moreira, B., Scott, D., Brown, I., Williams, A. R., Bates, P. A., Smyth, J. F., & Gabra, H. (2003). OPCML at 11q25 is epigenetically inactivated and has tumor-suppressor function in epithelial ovarian cancer. Nature Genetics, 34(3), 337–343. https://doi.org/10.1038/ng1183

Contreras-Moreira, B., Fitzjohn, P. W., Offman, M., Smith, G. R., & Bates, P. A. (2003). Novel use of a genetic algorithm for protein structure prediction: Searching template and sequence alignment space. Proteins: Structure, Function, and Genetics, 53(S6), 424–429. https://doi.org/10.1002/prot.10549

Contreras-Moreira, B., Fitzjohn, P. W., & Bates, P. A. (2003). In silico Protein Recombination: Enhancing Template and Sequence Alignment Selection for Comparative Protein Modelling. Journal of Molecular Biology, 328(3), 593–608. https://doi.org/10.1016/s0022-2836(03)00309-7

Jiménez, J. L., Smith, G. R., Contreras-Moreira, B., Sgouros, J. G., Meunier, F. A., Bates, P. A., & Schiavo, G. (2003). Functional Recycling of C2 Domains Throughout Evolution: A Comparative Study of Synaptotagmin, Protein Kinase C and Phospholipase C by Sequence, Structural and Modelling Approaches. Journal of Molecular Biology, 333(3), 621–639. https://doi.org/10.1016/j.jmb.2003.08.052

Contreras-Moreira, B., & Bates, P. A. (2002). Domain Fishing: a first step in protein comparative modelling. Bioinformatics, 18(8), 1141–1142. https://doi.org/10.1093/bioinformatics/18.8.1141

• Pangenomics and transcriptional regulation of grasses
• High-resolution agroclimatic indices for field trials and adaptation studies
• Evolutionary and structural analysis of ductile proteins (IDPs) and flavoenzymes