Computational & structural biology publications

Home

Members

Publications

Software

Material educativo

Blog

Articles & preprints

• Bruno Contreras Moreira: scholar digital.csic ORCiD
• Inmaculada Yruela: scholar digital.csic ORCiD

Books and chapters

1. Contreras-Moreira B, Rodríguez del Río A, Cantalapiedra CP, Sancho R, Vinuesa P (2022) Pangenome Analysis of Plant Transcripts and Coding Sequences. In: Pereira-Santana A, Gamboa-Tuz SD, Rodríguez-Zapata LC (eds) Plant Comparative Genomics. Methods in Molecular Biology, vol 2512. Humana, New York, NY. 10.1007/978-1-0716-2429-6_9.
2. Contreras-Moreira B, Naamati G, Rosello M, Allen JE, Hunt SE, Muffato M, Gall A, Flicek P (2022) Scripting Analyses of Genomes in Ensembl Plants. In: Edwards D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. 10.1007/978-1-0716-2067-0_2.
3. Contreras-Moreira B (2018) Algoritmos en Bioinformática Estructural. 10.20350/digitalcsic/8544.
4. 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)
5. 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)
6. 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)
7. Yruela I (2016) Las proteínas dúctiles. Editorial CSIC y Catarata. ISBN: 978-84-00-10055-1. Pages: 94 (comprar)
8. 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)
9. 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)
10. Yruela I (2014) Proteínas desordenadas. In Bioinformática con Ñ, edited by Sebastián A. and Pascual-García A. Zenodo (doi:10.5281/zenodo.1066352)
11. 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)
12. 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)
13. 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)
14. 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)
15. 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, author’s PDF)
16. 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)
17. 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. (PDF)

PhD & Master theses

• Ksouri N (2024) Bioinformatics for Advancing Peach Genetic Improvements. PhD thesis, Universidad de Zaragoza (PDF).
• María Ángeles Decena (2023) Evolution of allopolyploidy in species of the model genus Brachypodium (Poaceae) using genomic, transcriptomic, cytogenetic and phenotypic approaches. PhD thesis, Universidad de Zaragoza (PDF).
• Abdalrahem A (2022) Exploring the panregulome of grasses with model species Brachypodium distachyon. Masters thesis, CIHEAM-IAMZ & Universidad de Lleida (PDF).
• Sancho Cohen R (2018) Genome annotation, comparative genomics and evolution of the model grass genus Brachypodium (Poaceae). PhD thesis, Universidad de Zaragoza (PDF).
• de Anda Torres VY (2018) La metagenómica como herramienta de conservación de Cuatro Ciénegas Coahuila: el caso del ciclo del azufre. PhD thesis, Universidad Nacional Autónoma de México (PDF).
• Montardit F (2018) Genomic delimitation of proximal promoter regions: three approaches in Prunus persica. Masters thesis, CIHEAM-IAMZ & Universidad de Lleida (PDF).
• Cantalapiedra CP (2016) Accessing genetic variability in Spanish barleys through high-throughput sequencing. PhD thesis, Universitat Autonoma de Barcelona (PDF).
• Ksouri N (2016) Transcriptional Responses in Prunus persica under Conditions of Drought Stress using RNA Sequencing. Master thesis, CIHEAM-Universitat de Lleida (PDF, talk).
• Contreras-Moreira B (2004). Algorithms for protein comparative modelling and some evolutionary implications. PhD thesis (Biochemistry), University of London. (PDF, talk).
• Yruela I (1989). Geoquímica orgánica de cuencas lacustres y marismas. Tesis doctoral, Universidad de Sevilla. (PDF).

Supplementary materials of publications

• homeobox interface data from Sebastián A, Cantalapiedra CP 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

• suppl, alignments and superimpositions from Contreras-Moreira B, Sancho J, Espinosa Angarica V. (2010) Comparison of DNA binding across protein superfamilies. Proteins, 78(1):52-62

• network markers from Janga SC 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

• prok_specificity_suppl from 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

• footprints from Contreras-Moreira B and Collado-Vides J (2006) Comparative footprinting of DNA-binding proteins. Bioinformatics, 22(14): e74