laboratory of computational & structural biology

Peer-reviewed articles

  1. Yruela I, Contreras-Moreira B, Dunker AK and Niklas KJ (2018) Evolution of Protein Ductility in Duplicated Genes of Plants. Front. Plant Sci. doi:10.3389/fpls.2018.01216

  2. Nguyen NTT*, Contreras-Moreira B*, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, 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, doi:10.1093/nar/gky317

  3. Casas AM, Contreras-Moreira B, Cantalapiedra CP, Sakuma S, Gracia MP, Moralejo M, Molina-Cano JL, Komatsuda T, Igartua E (2018) Resequencing Vrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike. Molecular Breeding, doi:10.1007/s11032-018-0816-z, ENA sequences: LT727691-LT727723

  4. Vinuesa P, Ochoa L, 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, doi:10.3389/fmicb.2018.00771 (Docker image, GitHub)

  5. Niklas KJ, Dunker AK, Yruela I (2018) The evolutionary origins of cell type diversification and the role of intrinsically disordered proteins. Journal of Experimental Botany, 69(7): 1437-46 doi:10.1093/jxb/erx493

  6. Gordon SP, Contreras-Moreira B, Woods DP, 21+, Catalan P, Vogel JP (2017) Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications, 2184 doi:10.1038/s41467-017-02292-8

  7. Sancho R, Cantalapiedra CP, López-Alvarez D, Gordon SP, Vogel JP, Pilar 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, doi:10.1111/nph.14926 (PDF, preprint, ENA sequences: LT222229-LT222230 & LT558582-LT558636)

  8. Sein-Echaluce VC, Pallarés MC, Lostao A, Yruela I, Velázquez-Campo A, Peleato ML, Fillat MF (2017) Molecular basis for the integration of environmental signals by FurB from Anabaena sp. PCC 7120. Biochemical Journal, doi:10.1042/BCJ20170692 (PDF)

  9. De Anda V*, Zapata-Peñasco I, Poot-Hernandez AC, Eguiarte LE,Contreras-Moreira B* and Valeria Souza V* (2017) MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. GigaScience, (* corresponding author, doi:10.1093/gigascience/gix096, talk)

  10. Cantalapiedra CP, Garcia-Pereira MJ, Gracia MP, Igartua E, Casas AM, Contreras-Moreira B (2017) Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace. Front. Plant Sci. | doi: 10.3389/fpls.2017.00647 (PDF, ENA sequences: PRJEB12540)

  11. Yruela I, Oldfield CJ, Niklas KJ, Dunker AK (2017) Evidence for a strong correlation between transcription factor protein disorder and organismic complexity. Genome Biol Evol doi: 10.1093/gbe.evx073 (PDF)

  12. Contreras-Moreira B, Cantalapiedra CP, García-Pereira M, Gordon SP, Vogel JP, Igartua E, Casas AM, Vinuesa P (2017) Analysis of plant pan-genomes and transcriptomes with GET_HOMOLOGUES-EST, a clustering solution for sequences of the same species. Front. Plant Sci. 8:184. doi: 10.3389/fpls.2017.00184 (PDF)

  13. Yruela I, Contreras-Moreira B, Magalhaes C, Osorio NS, Gonzalo-Asensio J (2016) Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition. Genome Biology and Evolution doi: 10.1093/gbe/evw279 (PDF)

  14. Bernal-Bayard P, Puerto-Galá L, Yruela I et al. (2017) The photosynthetic cytochrome c550 from the diatom Phaeodactylum tricornutum. Photosynthesis Research doi:10.1007/s11120-016-0327-x (PDF)

  15. Ksouri N, Jiménez S, Wells CE, Contreras-Moreira B*, Gogorcena Y* (2016). Transcriptional Responses in root and leaf of Prunus persica Under Drought Stress Using RNA Sequencing. Front. Plant Sci. 7:1715. doi: 10.3389/fpls.2016.01715 (* corresponding author, PDF, transcripts)

  16. Gutierrez-Carbonell E, Takahashi D, Luthje S, Gonzalez-Reyes JA, Mongrand S, Contreras-Moreira B, Abadia A, Uemura M, Abadia J, Lopez-Millan AF (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. J. Proteome Res. doi: 10.1021/acs.jproteome.6b00026 (PDF)

  17. Perez-Palacios R, Macias-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 (PDF)

  18. Cantalapiedra CP, Contreras-Moreira B, Silvar C, Perovic D, Ordon F, Gracia MP, Igartua E, Casas A (2016) A cluster of NBS-LRR genes resides in a barley powdery mildew resistance QTL on 7HL. Plant Genome, doi: 10.3835/plantgenome2015.10.0101 (PDF)

  19. Valero-Gonzalez J, Leonhard-Melief C, Lira-Navarrete E, Jimenez-Oses G, Hernandez-Ruiz C, Pallares MC, Yruela I, Vasudevan D, Lostao A, Corzana F, Takeuchi H, Haltiwanger RS, Hurtado-Guerrero R (2016) A proactive role of water molecules in acceptor recognition by protein O-fucosyltransferase 2 Nature Chemical Biology, 12(4):240-6. doi:10.1038/nchembio.2019 (PDF)

  20. Medeot DB, Rivero MR, Cendoya E, Contreras-Moreira B, Rossi FA, Fischer SE, Becker A, Jofré E(2016) Sinorhizobium meliloti low molecular weight phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis. Microbiology, doi: 10.1099/mic.0.000239 (PDF)

  21. 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 10.1371/journal.pone.0141044 (PDF)

  22. Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon J, Delerce J, Spinelli L, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier L, Hernandez C, Thieffry D, Thomas-Chollier M and van Helden J. RSAT 2015: Regulatory Sequence Analysis Tools. Nucl Acids Res, 43(W1):W50-6 (PDF, RSAT::Plants).

  23. Yruela I (2015) Plant development regulation: Overview and perspectives. Journal of Plant Physiology 182:62-78 (PDF)

  24. Ceballos-Laita L, Gutierrez-Carbonell E, Lattanzio G, Vázquez S,Contreras-Moreira B, Abadía A, Abadía J, López-Millán AF. (2015) Changes in the protein profile ofBeta vulgaris leaf apoplastic fluid with Fe deficiency and Fe resupply. Frontiers in Plant Science 6:145 (PDF).

  25. Igartua E, Mansour E, Cantalapiedra CP, Contreras-Moreira B, Gracia MP, Fuster P, Escribano J, Molina-Cano JL, Moralejo M, Ciudad FJ, Thomas WTB, Karsai I and Casas A (2015) Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information. Molecular Breeding, 35:11 (PDF)

  26. Cantalapiedra CP, Boudiar R, Casas AM, Igartua E and Contreras-Moreira B (2015) BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley. Molecular Breeding, 35:13 (PDF)

  27. Dubos C, Kelemen Z, Sebastián A, Bulow 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, 15:317 (PDF, poster)

  28. Ito S, Magalska A, Alcaraz-Iborra M, Lopez-Atalaya JP, Rovira V, Contreras-Moreira B, Lipinski M, Olivares R, Martinez-Hernandez J, Ruszczycki B, Lujan R, Geijo-Barrientos E, Wilczynski GM and Barco A (2014) Loss of neuronal 3D chromatin organization causes transcriptional and behavioural deficits related to serotonergic dysfunction. Nature Communications, 5:4450 (doi:10.1038/ncomms545015:317, PDF)

  29. Loscos J, Igartua E, Contreras-Moreira B, Gracia MP and Casas AM (2014) HvFT1 polymorphism and effect – survey of barley germplasm and expression analysis Front. Plant Sci., doi: 10.3389/fpls.2014.00251 (PDF)

  30. Sebastián,A. and Contreras-Moreira,B. (2014) footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics, 30(2):258-265 (PDF, poster)

  31. Yruela,I. and Contreras-Moreira,B. (2013) Genetic recombination is associated with intrinsic disorder in plant proteomes. BMC Genomics, 14: 772 (PDF)

  32. Contreras-Moreira B, Vinuesa P. (2013) GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pan-genome analysis. Appl Environ Microbiol, 79:24 7696-7701 (PDF)

  33. Hofmann K, Silvar C, Casas AM, Herz M, Büttner B, Gracia MP,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. Theor Appl Genet, Epub ahead of print (PDF)

  34. Yruela,I. (2013) Transition metals in plant photosynthesis. Metallomics., 5(9):1090-109. (PDF)

  35. Serra,T.S., Figueiredo,D.D., Cordeiro,A.M., Almeida,D.M., Louren¸o,T., Abreu,I.A., Sebastián,A, Fernandes,L., Contreras-Moreira,B.,Oliveira,M.M. and Saibo,N.J.M. (2013) OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors. Plant Mol. Biol., 82 (4-5): 439-455 (PDF)

  36. Sebastián,A. and Contreras-Moreira,B. (2013) The twilight zone of cis element alignments. Nucleic Acids Research, 41(3): 1438-1449 (PDF,TFcompare)

  37. Yruela,I. and Contreras-Moreira,B. (2012) Protein disorder in plants: a view from the chloroplast BMC Plant Biology, 12:165 (PDF)

  38. Casas,A., Dejemel,A., Ciudad,F., Yahiaoui,S., Ponce,L., Contreras-Moreira,B., Gracia,M.P., Lasa,J.M. and Igartua,E. (2011) HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys. Theoretical and Applied Genetics, 122:1293-1304 (PDF, suppl)

  39. Yruela,I., Arilla-Luna,S., Medina,M. and Contreras-Moreira,B. (2010) Evolutionary divergence of chloroplast FAD synthetase proteins. BMC Evolutionary Biology, 10:311 (PDF)

  40. Janga,S.C. and 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 (PDF,suppl)

  41. Contreras-Moreira,B. (2010) 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic Acids Research, 38:D91-D97 (PDF, talk, interface video)

  42. Contreras-Moreira,B., Sancho,J., Espinosa Angarica,V. (2010) Comparison of DNA binding across protein superfamilies. Proteins, 78(1):52-62 (PDF,talk)

  43. 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. doi:10.1371/journal.pone.0007526 (PDF)

  44. Contreras-Moreira,B., Sachman-Ruiz,B., Figueroa-Palacios,I., and 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 issue):W95-W100 (PDF, PlantGEM poster)

  45. Espinosa Angarica,V., González Pérez,A., Vasconcelos,A.T., Collado-Vides,J. and Contreras-Moreira,B. (2008) Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics, 9:436. (PDF,talk,PWMs)

  46. Vinuesa,P., Rojas-Jiménez,K., Contreras-Moreira,B., Mahna,S.K., Prasad,B.N., Moe,H., Selvaraju,S.B., Thierfelder,H., and Werner,D. (2008) Multilocus Sequence Analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent. Appl. Environ. Microbiol., 74:6987-6996 (PDF)

  47. Lozada-Chávez,I., Espinosa Angarica,V., Collado-Vides,J. and Contreras-Moreira,B. (2008) The role of DNA-binding specificity in the evolution of bacterial regulatory networks. Journal of Molecular Biology, 379(3):627-43. (PDF, suppl, ISSOL2008 poster & abstract)

  48. Gama-Castro,S., Jiménez-Jacinto,V., Peralta-Gil,M., Santos-Zavaleta,A., Peñaloza-Spinola,M.I., Contreras-Moreira,B. [..] & Collado-Vides,J. (2008) 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: D120-D124 (PDF)

  49. Han, R., Leo-Macias, A., Zerbino, D., Bastolla, U., Contreras-Moreira, B. and Ortiz, A.R.(2007) An efficient conformational sampling method for homology modelling. Proteins, 71(1): 175-188 (PDF)

  50. Contreras-Moreira, B., Branger, P.A. and Collado-Vides, J. (2007) TFmodeller: comparative modelling of protein-DNA complexes. Bioinformatics, 23(13): 1694-1696 (PDF, suppl, poster)

  51. Contreras-Moreira, B. and Collado-Vides, J. (2006) Comparative footprinting of DNA-binding proteins. Bioinformatics, 22(14): e74.(PDF, talk, poster, suppl)

  52. Contreras-Moreira, B., Ezkurdia, I., Tress, M.L. and Valencia,A. (2005) Empirical limits for template-based protein structure prediction: the CASP5 example. FEBS Letters, 579(5): 1203-1207.(PDF)

  53. Smith, G.R.*, Contreras-Moreira, B.*, Zhang, X. and 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 (* joint first authors, PDF) (* joint first authors)

  54. Contreras-Moreira, B., Fitzjohn, P.W., Offman, M., Smith, G.R. and Bates, P.A. (2003) Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space. Proteins, 53 (S6): 424-429. (PDF, talk)

  55. Contreras-Moreira, B.*, Jonsson, P.F.* and Bates, P.A. (2003). Structural context to exons in protein domains: implications for protein modelling and design. Journal of Molecular Biology,333: 1057-1071. (PDF) (* joint first authors)

  56. Jimenez, J.L., Smith, G.R., Contreras-Moreira, B., Sgouros, J.G.,Meunier, F.A., Bates P.A. and Schiavo, G. (2003). A comparative study of synaptotagmin, protein kinase C and phosholipase C by sequence, structural and modelling approaches. Journal of Molecular Biology,333: 621-639. (PDF)

  57. 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. and Gabra,H. (2003). OPCML at 11q25 is epigenetically inactivated and has tumor-suppressor function in epithelial ovarian cancer. Nature Genetics, 34: 337-343. (PDF)

  58. Contreras-Moreira,B., Fitzjohn,P.W. and Bates,P.A. (2003). In silico Protein Recombination: enhancing template and sequence alignment selection for comparative protein modelling. Journal of Molecular Biology,328: 593-608.(PDF,talk)

  59. Contreras-Moreira,B., Fitzjohn,P.W. and Bates,P.A. (2002). Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era. Applied Bioinformatics,1(4);177-190.(PDF)

  60. Contreras-Moreira,B. and Bates,P.A. (2002). Domain Fishing: a first step in protein comparative modelling. Bioinformatics 18: 1141-1142. (PDF,talk)

Books and chapters

  1. Contreras-Moreira B (2018) Algoritmos en Bioinformática Estructural. doi:10.20350/digitalcsic/8544.

  2. Contreras-Moreira B, Castro-Mondragon J, Rioualen C, Cantalapiedra CP, van Helden J (2016) RSAT::Plants: Motif Discovery within Clusters of Upstream Sequences in Plant Genomes. In Plant Synthetic Promoters: Methods and Protocols, edited by Hehl R. Methods in Molecular Biology, 1482:279-95 (PDF, author's PDF)

  3. Castro-Mondragon J, Rioualen C, Contreras-Moreira B, van Helden J (2016) RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes. In Plant Synthetic Promoters: Methods and Protocols, edited by Hehl R. Methods in Molecular Biology, 1482:297-322 (PDF, author's PDF)

  4. Contreras-Moreira B and Sebastian A (2016) footprintDB: analysis of plant cis regulatory elements, transcription factors and binding interfaces. In Plant Synthetic Promoters: Methods and Protocols, edited by Hehl R. Methods in Molecular Biology, 1482:259-77 (PDF, author's PDF)

  5. Yruela I(2016) Las proteínas dúctiles. Editorial CSIC y Catarata. ISBN: 978-84-00-10055-1. Pages: 94 (comprar)

  6. Vinuesa P and Contreras-Moreira B (2015) Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids. In Bacterial Pangenomics, edited by A Mengoni, M Galardini and M Fondi. Methods in Molecular Biology, 1231: 203-232. (PDF)

  7. Vinuesa P, Contreras-Moreira B (2015) Chapter 27: Pangenomic analysis of the Rhizobiales using the GET_HOMOLOGUES software package. In Biological Nitrogen Fixation 7 (I), p271-80, Frans J de Bruijn (ed). Wiley. (PDF)

  8. Yruela I (2014) Proteínas desordenadas. In Bioinformática con Ñ, edited by Sebastián A. and Pascual-García A. Zenodo (doi:10.5281/zenodo.1066352)

  9. Yruela I, Sebastián A (2014) Macromoléculas biológicas: proteínas, DNA y RNA. In Bioinformática con Ñ, edited by Sebastián A. and Pascual-García A. Zenodo (doi:10.5281/zenodo.1067867)

  10. Sebastián A (2014) Análisis de secuencias biológicas. In Bioinformática con Ñ, edited by Sebastián A. and Pascual-García A. Zenodo (doi:10.5281/zenodo.1065598)

  11. Sebastián A, Fernández JM (2014) Computación paralela y clústeres de cálculo. In Bioinformática con Ñ, edited by Sebastián A. and Pascual-García A. Zenodo (doi:10.5281/zenodo.1065592)

  12. Fernández JM, Sebastián A (2014) Gestión de bibliografía e información y escritura de artículos científicos. In Bioinformática con Ñ, edited by Sebastián A. and Pascual-García A. Zenodo (doi:10.5281/zenodo.1065035)

  13. Sebastián,A., Cantalapiedra,C.P. and Contreras-Moreira,B. (2012) Interface similarity improves comparison of DNA-binding proteins: the Homeobox example. Lecture Notes in Computer Science, 6620/2012:72-82 (PDF, authors' PDF, suppl)

  14. Sachman-Ruiz,B. Contreras-Moreira,B., Zozaya,E., Martínez-Garza,C. and Vinuesa,P. (2011) primers4clades, a web server to design lineage-specfic PCR primers for gene-targeted metagenomics. Chapter 51 in Frans J. de Bruijn (ed.), Handbook of Molecular Microbial Ecology vol.I: Metagenomics and Complementary Approaches, (Google books,Wiley)

  15. Abascal F, Alonso-Allende R, Blaschke C, Contreras-Moreira B [...] and Valencia A (2001) Bioinformatics For Functional and Structural Genomics at the Protein Design group, CNB-CSIC. In Rita Casadio, Lanfranco Masotti (ed) Protein Sequence Analysis In The Post-Genomic Era: 149-165. CLUEB.

PhD & Master theses