Contreras-Moreira, B., Sharma, E., Saraf, S., Naamati, G., Gupta, P., Elser, J., Chebotarov, D., Chougule, K., Lu, Z., Wei, S., Olson, A., Tsang, I., Lodha, D., Zhou, Y., Yu, Z., Zhao, W., Zhang, J., Amberkar, S., Sue-Ob, K., … Jones, A. R. (2025). A pan-gene catalogue of Asian cultivated rice. https://doi.org/10.1101/2025.02.17.638606

Montardit-Tarda, F., Puyó, I., Contreras-Moreira, B., Karsai, I., Borrill, P., Casas, A. M., & Igartua, E. (2025). Vernalization regulatory network identifies potential novel functions forZCCTgenes withinHvVRN2. https://doi.org/10.1101/2025.04.29.651237

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

Contreras-Moreira, B., Saraf, S., Naamati, G., Casas, A. M., Amberkar, S. S., Flicek, P., Jones, A. R., & Dyer, S. (2023). Calling pangenes from plant genome alignments confirms presence-absence variation. https://doi.org/10.1101/2023.01.03.520531

Hurtado-Páez, U., Álvarez Zuluaga, N., Arango Isaza, R. E., Contreras-Moreira, B., Rouzaud, F., & Robledo, J. (2023). Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.1076797

Boden, S. A., McIntosh, R. A., Uauy, C., Krattinger, S. G., Dubcovsky, J., Rogers, W. J., Xia, X. C., Badaeva, E. D., Bentley, A. R., Brown-Guedira, G., Caccamo, M., Cattivelli, L., Chhuneja, P., Cockram, J., Contreras-Moreira, B., Dreisigacker, S., Edwards, D., González, F. G., … Guzmán, C. (2023). Updated guidelines for gene nomenclature in wheat. Theoretical and Applied Genetics, 136(4). https://doi.org/10.1007/s00122-023-04253-w

Ksouri, N., Sánchez, G., Forcada, C. F. i, Contreras-Moreira, B., & Gogorcena, Y. (2023). ddRAD-seq-derived SNPs reveal novel association signatures for fruit-related traits in peach. https://doi.org/10.1101/2023.07.31.551252

Contreras-Moreira, B., Saraf, S., Naamati, G., Casas, A. M., Amberkar, S. S., Flicek, P., Jones, A. R., & Dyer, S. (2023). GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. Genome Biology, 24(1). https://doi.org/10.1186/s13059-023-03071-z

Rodríguez del Río, Á., Monteagudo, A., Contreras-Moreira, B., Kiss, T., Mayer, M., Karsai, I., Igartua, E., & Casas, A. M. (2023). Diversity of gene expression responses to light quality in barley. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-44263-8

Medeot, D., Sannazzaro, A., Estrella, M. J., Torres Tejerizo, G., Contreras-Moreira, B., Pistorio, M., & Jofré, E. (2023). Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-49194-y

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

Contreras-Moreira, B., Naamati, G., Rosello, M., Allen, J. E., Hunt, S. E., Muffato, M., Gall, A., & Flicek, P. (2022). Scripting Analyses of Genomes in Ensembl Plants. Plant Bioinformatics, 27–55. https://doi.org/10.1007/978-1-0716-2067-0_2

Santana-Garcia, W., Castro-Mondragon, J. A., Padilla-Gálvez, M., Nguyen, N. T. T., Elizondo-Salas, A., Ksouri, N., Gerbes, F., Thieffry, D., Vincens, P., Contreras-Moreira, B., van Helden, J., Thomas-Chollier, M., & Medina-Rivera, A. (2022). RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Research, 50(W1), W670–W676. https://doi.org/10.1093/nar/gkac312

Sancho, R., Catalán, P., Contreras‐Moreira, B., Juenger, T. E., & Des Marais, D. L. (2022). Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon. Molecular Ecology, 31(20), 5285–5306. Portico. https://doi.org/10.1111/mec.16661

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

Sancho, R., Catalán, P., Contreras-Moreira, B., Juenger, T. E., & Des Marais, D. L. (2021). Patterns of pan-genome occupancy and gene co-expression under water-deficit in Brachypodium distachyon. https://doi.org/10.1101/2021.07.21.453242

Monteagudo, A., del Río, Á. R., Contreras-Moreira, B., Kiss, T., Mayer, M., Karsai, I., Igartua, E., & Casas, A. M. (2021). Light spectra trigger divergent gene expression in barley cultivars. https://doi.org/10.1101/2021.02.03.429565

Contreras-Moreira, B., Filippi, C. V., Naamati, G., Girón, C. G., Allen, J. E., & Flicek, P. (2021). Efficient masking of plant genomes by combining kmer counting and curated repeats. https://doi.org/10.1101/2021.03.22.436504

Ksouri, N., Castro-Mondragón, J. A., Montardit-Tarda, F., van Helden, J., Contreras-Moreira, B., & Gogorcena, Y. (2021). Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example. Plant Physiology, 185(3), 1242–1258. https://doi.org/10.1093/plphys/kiaa091

Decena, M. A., Galvez-Rojas, S., Agostini, F., Sancho, R., Contreras-Moreira, B., Des Marais, D. L., Hernández, P., & Catalán, P. (2021). Evolution and functional dynamics of dehydrins in model Brachypodium grasses. https://doi.org/10.1101/2021.09.03.458816

Contreras‐Moreira, B., Filippi, C. V., Naamati, G., García Girón, C., Allen, J. E., & Flicek, P. (2021). K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes. The Plant Genome, 14(3). Portico. https://doi.org/10.1002/tpg2.20143

Decena, M. A., Gálvez-Rojas, S., Agostini, F., Sancho, R., Contreras-Moreira, B., Des Marais, D. L., Hernandez, P., & Catalán, P. (2021). Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses. Plants, 10(12), 2664. https://doi.org/10.3390/plants10122664

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

Ksouri, N., Castro-Mondragón, J. A., Montardit-Tardà, F., van Helden, J., Contreras-Moreira, B., & Gogorcena, Y. (2020). Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model. https://doi.org/10.1101/2020.02.28.970137

Filippi, C. V., Merino, G. A., Montecchia, J. F., Aguirre, N. C., Rivarola, M., Naamati, G., Fass, M. I., Álvarez, D., Di Rienzo, J., Heinz, R. A., Contreras Moreira, B., Lia, V. V., & Paniego, N. B. (2020). Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections. Genes, 11(3), 283. https://doi.org/10.3390/genes11030283

Adamski, N. M., Borrill, P., Brinton, J., Harrington, S. A., Marchal, C., Bentley, A. R., Bovill, W. D., Cattivelli, L., Cockram, J., Contreras-Moreira, B., Ford, B., Ghosh, S., Harwood, W., Hassani-Pak, K., Hayta, S., Hickey, L. T., Kanyuka, K., King, J., Maccaferrri, M., … Uauy, C. (2020). A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. ELife, 9. CLOCKSS. https://doi.org/10.7554/elife.55646

Gordon, S. P., Contreras-Moreira, B., Levy, J. J., Djamei, A., Czedik-Eysenberg, A., Tartaglio, V. S., Session, A., Martin, J., Cartwright, A., Katz, A., Singan, V. R., Goltsman, E., Barry, K., Dinh-Thi, V. H., Chalhoub, B., Diaz-Perez, A., Sancho, R., Lusinska, J., Wolny, E., … Vogel, J. P. (2020). Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17302-5

Igartua, E., Contreras-Moreira, B., & Casas, A. M. (2020). TB1: from domestication gene to tool for many trades. Journal of Experimental Botany, 71(16), 4621–4624. https://doi.org/10.1093/jxb/eraa308

Contreras‐Moreira, B., Serrano‐Notivoli, R., Mohammed, N. E., Cantalapiedra, C. P., Beguería, S., Casas, A. M., & Igartua, E. (2019). Genetic association with high‐resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula. Molecular Ecology, 28(8), 1994–2012. Portico. https://doi.org/10.1111/mec.15009

Monteagudo, A., Casas, A. M., Cantalapiedra, C. P., Contreras-Moreira, B., Gracia, M. P., & Igartua, E. (2019). Harnessing Novel Diversity From Landraces to Improve an Elite Barley Variety. Frontiers in Plant Science, 10. https://doi.org/10.3389/fpls.2019.00434

Santana-Garcia, W., Rocha-Acevedo, M., Ramirez-Navarro, L., Mbouamboua, Y., Thieffry, D., Thomas-Chollier, M., Contreras-Moreira, B., van Helden, J., & Medina-Rivera, A. (2019). RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding. https://doi.org/10.1101/623090

Howe, K. L., Contreras-Moreira, B., De Silva, N., Maslen, G., Akanni, W., Allen, J., Alvarez-Jarreta, J., Barba, M., Bolser, D. M., Cambell, L., Carbajo, M., Chakiachvili, M., Christensen, M., Cummins, C., Cuzick, A., Davis, P., Fexova, S., Gall, A., George, N., … Flicek, P. (2019). Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Research, 48(D1), D689–D695. https://doi.org/10.1093/nar/gkz890

Santana-Garcia, W., Rocha-Acevedo, M., Ramirez-Navarro, L., Mbouamboua, Y., Thieffry, D., Thomas-Chollier, M., Contreras-Moreira, B., van Helden, J., & Medina-Rivera, A. (2019). RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding. Computational and Structural Biotechnology Journal, 17, 1415–1428. https://doi.org/10.1016/j.csbj.2019.09.009

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

De Anda, V., Zapata-Peñasco, I., Blaz, J., Poot-Hernández, A. C., Contreras-Moreira, B., González-Laffitte, M., Gámez-Tamariz, N., Hernández-Rosales, M., Eguiarte, L. E., & Souza, V. (2018). Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach. Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.02606

Casas, A. M., Contreras-Moreira, B., Cantalapiedra, C. P., Sakuma, S., Gracia, M. P., Moralejo, M., Molina-Cano, J. L., Komatsuda, T., & Igartua, E. (2018). Resequencing theVrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike. Molecular Breeding, 38(5). https://doi.org/10.1007/s11032-018-0816-z

Nguyen, N. T. T., Contreras-Moreira, B., Castro-Mondragon, J. A., Santana-Garcia, W., Ossio, R., Robles-Espinoza, C. D., Bahin, M., Collombet, S., Vincens, P., Thieffry, D., van Helden, J., Medina-Rivera, A., & Thomas-Chollier, M. (2018). RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research, 46(W1), W209–W214. https://doi.org/10.1093/nar/gky317

Yruela, I., Contreras-Moreira, B., Dunker, A. K., & Niklas, K. J. (2018). Evolution of Protein Ductility in Duplicated Genes of Plants. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.01216

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

Yruela, I., Contreras-Moreira, B., Magalhães, C., Osório, N. S., & Gonzalo-Asensio, J. (2017). Mycobacterium tuberculosisComplex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition. Genome Biology and Evolution, evw279. https://doi.org/10.1093/gbe/evw279

Yruela, I., Contreras-Moreira, B., Magalhães, C., Osório, N. S., & Gonzalo-Asensio, J. (2017). Mycobacterium tuberculosisComplex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition. Genome Biology and Evolution, evw279. https://doi.org/10.1093/gbe/evw279

Contreras-Moreira, B., Cantalapiedra, C. P., García-Pereira, M. J., Gordon, S. P., Vogel, J. P., Igartua, E., Casas, A. M., & Vinuesa, P. (2017). Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.00184

Cantalapiedra, C. P., García-Pereira, M. J., Gracia, M. P., Igartua, E., Casas, A. M., & Contreras-Moreira, B. (2017). Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.00647

De Anda, V., Zapata-Peñasco, I., Contreras-Moreira, B., Poot-Hernandez, A. C., Eguiarte, L. E., & Souza, V. (2017). A new multi-genomic approach for the study of biogeochemical cycles at global scale: the molecular reconstruction of the sulfur cycle. https://doi.org/10.1101/148775

Gordon, S. P., Contreras-Moreira, B., Woods, D. P., Des Marais, D. L., Burgess, D., Shu, S., Stritt, C., Roulin, A. C., Schackwitz, W., Tyler, L., Martin, J., Lipzen, A., Dochy, N., Phillips, J., Barry, K., Geuten, K., Budak, H., Juenger, T. E., Amasino, R., … Vogel, J. P. (2017). Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-02292-8

Sancho, R., Cantalapiedra, C. P., López‐Alvarez, D., Gordon, S. P., Vogel, J. P., Catalán, P., & Contreras‐Moreira, B. (2017). Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes. New Phytologist, 218(4), 1631–1644. Portico. https://doi.org/10.1111/nph.14926

Ksouri, N., Jiménez, S., Wells, C. E., Contreras-Moreira, B., & Gogorcena, Y. (2016). Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing. Frontiers in Plant Science, 7. https://doi.org/10.3389/fpls.2016.01715

Castro-Mondragon, J. A., Rioualen, C., Contreras-Moreira, B., & van Helden, J. (2016). RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes. Plant Synthetic Promoters, 297–322. https://doi.org/10.1007/978-1-4939-6396-6_19

Contreras-Moreira, B., Castro-Mondragon, J. A., Rioualen, C., Cantalapiedra, C. P., & van Helden, J. (2016). RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes. Plant Synthetic Promoters, 279–295. https://doi.org/10.1007/978-1-4939-6396-6_18

Pérez-Palacios, R., Macías-Redondo, S., Climent, M., Contreras-Moreira, B., Muniesa, P., & Schoorlemmer, J. (2016). In Vivo Chromatin Targets of the Transcription Factor Yin Yang 2 in Trophoblast Stem Cells. PLOS ONE, 11(5), e0154268. https://doi.org/10.1371/journal.pone.0154268

Contreras-Moreira, B., & Sebastian, A. (2016). FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces. Plant Synthetic Promoters, 259–277. https://doi.org/10.1007/978-1-4939-6396-6_17

Cantalapiedra, C. P., Contreras‐Moreira, B., Silvar, C., Perovic, D., Ordon, F., Gracia, M. P., Igartua, E., & Casas, A. M. (2016). A Cluster of Nucleotide‐Binding Site–Leucine‐Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL. The Plant Genome, 9(2). Portico. https://doi.org/10.3835/plantgenome2015.10.0101

Medeot, D. B., Romina Rivero, M., Cendoya, E., Contreras-Moreira, B., Rossi, F. A., Fischer, S. E., Becker, A., & Jofré, E. (2016). Sinorhizobium meliloti low molecular mass phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis. Microbiology, 162(3), 552–563. https://doi.org/10.1099/mic.0.000239

Gutierrez-Carbonell, E., Takahashi, D., Lüthje, S., González-Reyes, J. A., Mongrand, S., Contreras-Moreira, B., Abadía, A., Uemura, M., Abadía, J., & López-Millán, A. F. (2016). A Shotgun Proteomic Approach Reveals That Fe Deficiency Causes Marked Changes in the Protein Profiles of Plasma Membrane and Detergent-Resistant Microdomain Preparations from Beta vulgaris Roots. Journal of Proteome Research, 15(8), 2510–2524. https://doi.org/10.1021/acs.jproteome.6b00026

Igartua, E., Mansour, E., Cantalapiedra, C. P., Contreras-Moreira, B., Gracia, M. P., Fuster, P., Escribano, J., Molina-Cano, J. L., Moralejo, M., Ciudad, F. J., Thomas, W. T. B., Karsai, I., & Casas, A. M. (2015). Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information. Molecular Breeding, 35(1). https://doi.org/10.1007/s11032-015-0194-8

Vinuesa, P., & Contreras-Moreira, B. (2015). Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids. Bacterial Pangenomics, 203–232. https://doi.org/10.1007/978-1-4939-1720-4_14

Cantalapiedra, C. P., Boudiar, R., Casas, A. M., Igartua, E., & Contreras-Moreira, B. (2015). BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley. Molecular Breeding, 35(1). https://doi.org/10.1007/s11032-015-0253-1

Kelemen, Z., Sebastian, A., Xu, W., Grain, D., Salsac, F., Avon, A., Berger, N., Tran, J., Dubreucq, B., Lurin, C., Lepiniec, L., Contreras-Moreira, B., & Dubos, C. (2015). Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast. PLOS ONE, 10(10), e0141044. https://doi.org/10.1371/journal.pone.0141044

Medina-Rivera, A., Defrance, M., Sand, O., Herrmann, C., Castro-Mondragon, J. A., Delerce, J., Jaeger, S., Blanchet, C., Vincens, P., Caron, C., Staines, D. M., Contreras-Moreira, B., Artufel, M., Charbonnier-Khamvongsa, L., Hernandez, C., Thieffry, D., Thomas-Chollier, M., & van Helden, J. (2015). RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Research, 43(W1), W50–W56. https://doi.org/10.1093/nar/gkv362

Vinuesa, P., & Contreras‐Moreira, B. (2015). Pangenomic Analysis of theRhizobialesUsing the GET_HOMOLOGUES Software Package. Biological Nitrogen Fixation, 271–280. Portico. https://doi.org/10.1002/9781119053095.ch27

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

Dubos, C., Kelemen, Z., Sebastian, A., Bülow, L., Huep, G., Xu, W., Grain, D., Salsac, F., Brousse, C., Lepiniec, L., Weisshaar, B., Contreras-Moreira, B., & Hehl, R. (2014). Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-317

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

Sebastian, A., & Contreras-Moreira, B. (2013). footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics, 30(2), 258–265. https://doi.org/10.1093/bioinformatics/btt663

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

Han, R., Leo‐Macias, A., Zerbino, D., Bastolla, U., Contreras‐Moreira, B., & Ortiz, A. R. (2007). An efficient conformational sampling method for homology modeling. Proteins: Structure, Function, and Bioinformatics, 71(1), 175–188. Portico. https://doi.org/10.1002/prot.21672

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

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