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Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula.

Contreras-Moreira B, Serrano-Notivoli R, Mohamed NE, Cantalapiedra CP, Beguería S, Casas AM, Igartua E.

Mol Ecol. 2019 Jan 7. doi: 10.1111/mec.15009. [Epub ahead of print]


Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach.

De Anda V, Zapata-Peñasco I, Blaz J, Poot-Hernández AC, Contreras-Moreira B, González-Laffitte M, Gámez-Tamariz N, Hernández-Rosales M, Eguiarte LE, Souza V.

Front Microbiol. 2018 Nov 28;9:2606. doi: 10.3389/fmicb.2018.02606. eCollection 2018.


Evolution of Protein Ductility in Duplicated Genes of Plants.

Yruela I, Contreras-Moreira B, Dunker AK, Niklas KJ.

Front Plant Sci. 2018 Aug 20;9:1216. doi: 10.3389/fpls.2018.01216. eCollection 2018.


RSAT 2018: regulatory sequence analysis tools 20th anniversary.

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.

Nucleic Acids Res. 2018 Jul 2;46(W1):W209-W214. doi: 10.1093/nar/gky317.


Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

Gordon SP, Contreras-Moreira B, Woods DP, Des Marais DL, Burgess D, Shu S, Stritt C, Roulin AC, Schackwitz W, Tyler L, Martin J, Lipzen A, Dochy N, Phillips J, Barry K, Geuten K, Budak H, Juenger TE, Amasino R, Caicedo AL, Goodstein D, Davidson P, Mur LAJ, Figueroa M, Freeling M, Catalan P, Vogel JP.

Nat Commun. 2017 Dec 19;8(1):2184. doi: 10.1038/s41467-017-02292-8.


Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes.

Sancho R, Cantalapiedra CP, López-Alvarez D, Gordon SP, Vogel JP, Catalán P, Contreras-Moreira B.

New Phytol. 2018 Jun;218(4):1631-1644. doi: 10.1111/nph.14926. Epub 2017 Dec 5.


MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle.

De Anda V, Zapata-Peñasco I, Poot-Hernandez AC, Eguiarte LE, Contreras-Moreira B, Souza V.

Gigascience. 2017 Nov 1;6(11):1-17. doi: 10.1093/gigascience/gix096.


Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace.

Cantalapiedra CP, García-Pereira MJ, Gracia MP, Igartua E, Casas AM, Contreras-Moreira B.

Front Plant Sci. 2017 May 1;8:647. doi: 10.3389/fpls.2017.00647. eCollection 2017.


Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species.

Contreras-Moreira B, Cantalapiedra CP, García-Pereira MJ, Gordon SP, Vogel JP, Igartua E, Casas AM, Vinuesa P.

Front Plant Sci. 2017 Feb 14;8:184. doi: 10.3389/fpls.2017.00184. eCollection 2017.


Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition.

Yruela I, Contreras-Moreira B, Magalhães C, Osório NS, Gonzalo-Asensio J.

Genome Biol Evol. 2016 Dec 1;8(12):3751-3764. doi: 10.1093/gbe/evw279.


Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing.

Ksouri N, Jiménez S, Wells CE, Contreras-Moreira B, Gogorcena Y.

Front Plant Sci. 2016 Nov 23;7:1715. eCollection 2016.


A Cluster of Nucleotide-Binding Site-Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL.

Cantalapiedra CP, Contreras-Moreira B, Silvar C, Perovic D, Ordon F, Gracia MP, Igartua E, Casas AM.

Plant Genome. 2016 Jul;9(2). doi: 10.3835/plantgenome2015.10.0101.


RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes.

Castro-Mondragon JA, Rioualen C, Contreras-Moreira B, van Helden J.

Methods Mol Biol. 2016;1482:297-322. doi: 10.1007/978-1-4939-6396-6_19.


RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.

Contreras-Moreira B, Castro-Mondragon JA, Rioualen C, Cantalapiedra CP, van Helden J.

Methods Mol Biol. 2016;1482:279-95. doi: 10.1007/978-1-4939-6396-6_18.


FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces.

Contreras-Moreira B, Sebastian A.

Methods Mol Biol. 2016;1482:259-77. doi: 10.1007/978-1-4939-6396-6_17.


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.

Gutierrez-Carbonell E, Takahashi D, Lüthje S, González-Reyes JA, Mongrand S, Contreras-Moreira B, Abadía A, Uemura M, Abadía J, López-Millán AF.

J Proteome Res. 2016 Aug 5;15(8):2510-24. doi: 10.1021/acs.jproteome.6b00026. Epub 2016 Jul 12.


In Vivo Chromatin Targets of the Transcription Factor Yin Yang 2 in Trophoblast Stem Cells.

Pérez-Palacios R, Macías-Redondo S, Climent M, Contreras-Moreira B, Muniesa P, Schoorlemmer J.

PLoS One. 2016 May 18;11(5):e0154268. doi: 10.1371/journal.pone.0154268. eCollection 2016.


Sinorhizobium meliloti low molecular mass phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis.

Medeot DB, Romina Rivero M, Cendoya E, Contreras-Moreira B, Rossi FA, Fischer SE, Becker A, Jofré E.

Microbiology. 2016 Mar;162(3):552-63. doi: 10.1099/mic.0.000239. Epub 2016 Jan 25.


Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast.

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.

PLoS One. 2015 Oct 20;10(10):e0141044. doi: 10.1371/journal.pone.0141044. eCollection 2015.


RSAT 2015: Regulatory Sequence Analysis Tools.

Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J.

Nucleic Acids Res. 2015 Jul 1;43(W1):W50-6. doi: 10.1093/nar/gkv362. Epub 2015 Apr 22.


Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply.

Ceballos-Laita L, Gutierrez-Carbonell E, Lattanzio G, Vázquez S, Contreras-Moreira B, Abadía A, Abadía J, López-Millán AF.

Front Plant Sci. 2015 Mar 18;6:145. doi: 10.3389/fpls.2015.00145. eCollection 2015.


Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: a case study of pIncA/C plasmids.

Vinuesa P, Contreras-Moreira B.

Methods Mol Biol. 2015;1231:203-32. doi: 10.1007/978-1-4939-1720-4_14.


Loss of neuronal 3D chromatin organization causes transcriptional and behavioural deficits related to serotonergic dysfunction.

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, Barco A.

Nat Commun. 2014 Jul 18;5:4450. doi: 10.1038/ncomms5450.


HvFT1 polymorphism and effect-survey of barley germplasm and expression analysis.

Loscos J, Igartua E, Contreras-Moreira B, Gracia MP, Casas AM.

Front Plant Sci. 2014 Jun 6;5:251. doi: 10.3389/fpls.2014.00251. eCollection 2014.


Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes.

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.

BMC Genomics. 2014 Apr 28;15:317. doi: 10.1186/1471-2164-15-317.


footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

Sebastian A, Contreras-Moreira B.

Bioinformatics. 2014 Jan 15;30(2):258-65. doi: 10.1093/bioinformatics/btt663. Epub 2013 Nov 14.


Genetic recombination is associated with intrinsic disorder in plant proteomes.

Yruela I, Contreras-Moreira B.

BMC Genomics. 2013 Nov 9;14:772. doi: 10.1186/1471-2164-14-772.


GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis.

Contreras-Moreira B, Vinuesa P.

Appl Environ Microbiol. 2013 Dec;79(24):7696-701. doi: 10.1128/AEM.02411-13. Epub 2013 Oct 4.


Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces.

Hofmann K, Silvar C, Casas AM, Herz M, Büttner B, Gracia MP, Contreras-Moreira B, Wallwork H, Igartua E, Schweizer G.

Theor Appl Genet. 2013 Dec;126(12):3091-102. doi: 10.1007/s00122-013-2196-4. Epub 2013 Sep 26.


OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors.

Serra TS, Figueiredo DD, Cordeiro AM, Almeida DM, Lourenço T, Abreu IA, Sebastián A, Fernandes L, Contreras-Moreira B, Oliveira MM, Saibo NJ.

Plant Mol Biol. 2013 Jul;82(4-5):439-55. doi: 10.1007/s11103-013-0073-9. Epub 2013 May 24.


The twilight zone of cis element alignments.

Sebastian A, Contreras-Moreira B.

Nucleic Acids Res. 2013 Feb 1;41(3):1438-49. doi: 10.1093/nar/gks1301. Epub 2012 Dec 24.


Protein disorder in plants: a view from the chloroplast.

Yruela I, Contreras-Moreira B.

BMC Plant Biol. 2012 Sep 13;12:165.


HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys.

Casas AM, Djemel A, Ciudad FJ, Yahiaoui S, Ponce LJ, Contreras-Moreira B, Gracia MP, Lasa JM, Igartua E.

Theor Appl Genet. 2011 May;122(7):1293-304. doi: 10.1007/s00122-011-1531-x. Epub 2011 Jan 30.


Evolutionary divergence of chloroplast FAD synthetase proteins.

Yruela I, Arilla-Luna S, Medina M, Contreras-Moreira B.

BMC Evol Biol. 2010 Oct 18;10:311. doi: 10.1186/1471-2148-10-311.


Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach.

Janga SC, Contreras-Moreira B.

Nucleic Acids Res. 2010 Nov;38(20):6841-56. doi: 10.1093/nar/gkq612. Epub 2010 Jul 14.


Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.

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 AM, Collado-Vides J, Morett E.

PLoS One. 2009 Oct 19;4(10):e7526. doi: 10.1371/journal.pone.0007526.


3D-footprint: a database for the structural analysis of protein-DNA complexes.

Contreras-Moreira B.

Nucleic Acids Res. 2010 Jan;38(Database issue):D91-7. doi: 10.1093/nar/gkp781. Epub 2009 Sep 18.


Comparison of DNA binding across protein superfamilies.

Contreras-Moreira B, Sancho J, Angarica VE.

Proteins. 2010 Jan;78(1):52-62. doi: 10.1002/prot.22525.


primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies.

Contreras-Moreira B, Sachman-Ruiz B, Figueroa-Palacios I, Vinuesa P.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W95-W100. doi: 10.1093/nar/gkp377. Epub 2009 May 21.


Prediction of TF target sites based on atomistic models of protein-DNA complexes.

Angarica VE, Pérez AG, Vasconcelos AT, Collado-Vides J, Contreras-Moreira B.

BMC Bioinformatics. 2008 Oct 16;9:436. doi: 10.1186/1471-2105-9-436.


Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent.

Vinuesa P, Rojas-Jiménez K, Contreras-Moreira B, Mahna SK, Prasad BN, Moe H, Selvaraju SB, Thierfelder H, Werner D.

Appl Environ Microbiol. 2008 Nov;74(22):6987-96. doi: 10.1128/AEM.00875-08. Epub 2008 Sep 12.


The role of DNA-binding specificity in the evolution of bacterial regulatory networks.

Lozada-Chávez I, Angarica VE, Collado-Vides J, Contreras-Moreira B.

J Mol Biol. 2008 Jun 6;379(3):627-43. doi: 10.1016/j.jmb.2008.04.008. Epub 2008 Apr 9.


RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, Bonavides-Martínez C, Abreu-Goodger C, Rodríguez-Penagos C, Miranda-Ríos J, Morett E, Merino E, Huerta AM, Treviño-Quintanilla L, Collado-Vides J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4. Epub 2007 Dec 23.


An efficient conformational sampling method for homology modeling.

Han R, Leo-Macias A, Zerbino D, Bastolla U, Contreras-Moreira B, Ortiz AR.

Proteins. 2008 Apr;71(1):175-88.


TFmodeller: comparative modelling of protein-DNA complexes.

Contreras-Moreira B, Branger PA, Collado-Vides J.

Bioinformatics. 2007 Jul 1;23(13):1694-6. Epub 2007 Apr 25.


Comparative footprinting of DNA-binding proteins.

Contreras-Moreira B, Collado-Vides J.

Bioinformatics. 2006 Jul 15;22(14):e74-80.


Empirical limits for template-based protein structure prediction: the CASP5 example.

Contreras-Moreira B, Ezkurdia I, Tress ML, Valencia A.

FEBS Lett. 2005 Feb 14;579(5):1203-7.


Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era.

Contreras-Moreira B, Fitzjohn PW, Bates PA.

Appl Bioinformatics. 2002;1(4):177-90. Review.


A link between sequence conservation and domain motion within the AAA+ family.

Smith GR, Contreras-Moreira B, Zhang X, Bates PA.

J Struct Biol. 2004 Apr-May;146(1-2):189-204.


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