Dr Narcis Fernandez-Fuentes

Dr Narcis Fernandez-Fuentes

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Narcis Fernandez-Fuentes is a Reader in Genomics/Bioinformatics. He received his M.Sc. degree in Biotechnology from the Universitat Autonoma de Barcelona, Spain, in 2001, and his PhD in Computational Biology from the same university in 2004.

During his PhD he was Marie Curie Training Fellow at the Structural Genomic Group in EMBL-EBI, Hinxton; Cambridge, U.K. where he worked with Prof. Liisa Holm; from Oct. 2002 to Apr. 2003 he worked with Prof. Michael J.E. Sternberg, Imperial College of London, U.K., supported by an EMBO and a FEBS short term fellowships and finally, between Oct. 2003 and Mar. 2004 he was visiting fellow at Dr. Fiser's Lab., Albert Einstein College of Medicine, NY, supported by Boehringer Ingelheim Fonds.

From 2004 to 2007 he was Research Associate at Dr. Andras Fiser Laboratory at Albert Einstein College of Medicine. From 2007 to 2011 he was a Lecturer funded by the RCUK Academic Fellow scheme at the Leeds Institute of Molecular Medicine were he established the Computational Biology Group within the Experimental Therapeutics Section.

In January 2012 he joined Aberystwyth University as Reader in Genomics/Bioinformatics.

Research

Bioinformatics and Structural Bioinformatics. Protein design. Structure-based analysis of protein-protein interactions. Databases and bioinformatics tools. SNPs modelling.

Our research interests relate to a number of areas within Bioinformatics. We have a long-standing interest in protein structure prediction and structure-to-function relationship. We work in the study of biomolecular interactions, modeling of protein complexes in genome-wide interactomes, modulation of protein-protein interactions and structure-based protein design. We are also interested in computational design of peptides for the modulation of protein interactions as potential therapeutic agents or diagnostic tools. In the area of Plant Bioinformatics, we are developing bioinformatics-based approaches to complement guide and improve plant-breeding programmes and to understand the underlying biological mechanisms liked to the response to abiotic stresses. We are also interested in the modelling of genetic variation, e.g. SNPs, and the assessment of functional impact at protein level. Finally, we work in close collaboration with experimental labs in a synergistic manner by applying or developing novel tools to address different research questions.

Publications

Draft Genome Assemblies of Xylose-Utilizing Candida tropicalis and Candida boidinii with Potential Application in Biochemical and Biofuel ProductionSomani, A., Smith, D., Hegarty, M., Fernandez-Fuentes, N., Ravella, S., Gallagher, J. & Bryant, D. 2018 In : Genome Announcements.6, 7, e01594-17
The rumen microbiome: an underexplored resource for novel antimicrobial discoveryOyama, L. B., Girdwood, S. E., Cookson, A. R., Fernandez-fuentes, N., Privé, F., Vallin, H. E., Wilkinson, T. J., Golyshin, P. N., Golyshina, O. V., Mikut, R., Hilpert, K., Richards, J., Wootton, M., Edwards, J. E., Maresca, M., Perrier, J., Lundy, F. T., Luo, Y., Zhou, M., Hess, M., Mantovani, H. C., Creevey, C. J. & Huws, S. A. 2017 In : npj Biofilms and Microbiomes.3, 1, 33
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structuresMarín-López, M. A., Planas-Iglesias, J., Aguiree-Plans, J., Bonet, J., Garcia-Garcia, J., Fernandez-Fuentes, . N. & Oliva, B. 2017 In : Bioinformatics.34, 4, p. 592-5987 p.
Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalisOyama, L. B., Crochet, J-A., Edwards, J. E., Girdwood, S., Cookson, A., Fernandez-Fuentes, N., Hilpert, K., Golyshin, P. N., Golyshina, O. V., Privé, F., Hess, M., Mantovani, H. C., Creevey, C. & Huws, S. 2017 In : Frontiers in Chemistry.5, 51
iFrag: A Protein-Protein Interface Prediction Server Based on Sequence FragmentsGarcia-Garcia, J., Valls-Comamala, V., Guney, E., Andreu, D., Muñoz , F. J., Fernandez-Fuentes, N. & Oliva, B. 2017 In : Journal of Molecular Biology.
MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteinsKara, A., Vickers, M., Swain, M., Whitworth, D. & Fernandez-Fuentes, N. 2016 In : Bioinformatics.32, 21, p. 3339-33413 p.
The GH51 α-l-arabinofuranosidase from Paenibacillus sp. THS1 is multifunctional, hydrolyzing main-chain and side-chain glycosidic bonds in heteroxylans.Bouraoui, H., Desrousseaux, M-L., Ioannou, E., Alvira, P., Manaï, M., Rémond, C., Dumon, C., Fernandez-Fuentes, N. & O'Donohue, M. J. 2016 In : Biotechnology for Biofuels.9, 140
InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical researchPoglayen, D., Marín-López, M. A., Bonet, J., Fornes, O., Garcia-Garcia, J., Planas-Iglesias, J., Segura, J., Oliva, B. & Fernandez-Fuentes, N. 2016 In : Biochemical Society Transactions.44, 3, p. 917-9248 p.
Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel TreatmentChalmers, I. W., Fitzsimmons, C. M., Brown, M., Pierrot, C., Jones, F. M., Wawrzyniak, J. M., Fernandez-Fuentes, N., Tukahebwa, E. M., Dunne, D. W., Khalife, J. & Hoffmann, K. F. 2015 In : PLoS Neglected Tropical Diseases.9, 7, p. e0003920
VORFFIP-Driven Dock: V-D2OCK, a Fast and Accurate Protein Docking StrategySegura, J., Marín-López, M. A., Jones, P. F., Oliva, B., Fernandez-fuentes, N. & Keskin, O. (ed.) 2015 In : PLoS One.10, 3, e0118107
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictorKara, A., Vickers, M., Swain, M., Whitworth, D. E. & Fernandez-Fuentes, N. 2015 In : BMC Bioinformatics.16, 1, 297
Frag’r’Us: Knowledge-based sampling of protein backbone conformations for de novo structure-based protein designBonet, J., Segura, J., Planas-Iglesias, J., Oliva, B. & Fernandez-Fuentes, N. 2014 In : Bioinformatics.30, 13, p. 1935-1936
Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complexSewell, H., Tanaka, T., Omari, K. E., Mancini, E. J., Cruz, A., Fernandez-Fuentes, N., Chambers, J. & Rabbitts, T. H. 2014 In : Scientific Reports.4, 3643
ArchDB 2014: Structural classification of loops in proteinsBonet, J., Planas-Iglesias, J., Garcia-Garcia, J., Marín-López, M. A., Fernandez-Fuentes, N. & Oliva, B. 2014 In : Nucleic Acids Research.42, D1, p. D315-D319
Peptides: minimal drug surrogates to interrogate and interfere with protein functionCruz-Migoni, A., Fernandez-Fuentes, N. & Rabbitts, T. H. 2013 In : MedChemComm.4, p. 1218-1221
A modular perspective of protein structures: application to fragment based loop modelingFernandez-Fuentes, N. & Fiser, A. 2013 Protein Supersecondary Structures. Kister, A. E. (ed.). Springer Nature, Vol. 932, p. 141-15818 p. (Methods in Molecular Biology; vol. 932)
A holistic in silico approach to predict functional sites in protein structuresSegura, J., Jones, P. F. & Fernandez-Fuentes, N. 2012 In : Bioinformatics.28, 14, p. 1845-1850
Computational Tools and Databases for the Study and Characterization of Protein Interactions.Segura, J., Blas Pastor, J. R. & Fernandez-Fuentes, N. 2012 Protein-Protein Interactions - Computational and Experimental Tools. Cai, W. & Hong, H. (eds.). Chapter 19 ed.InTechOpen, p. 379-40426 p. (Biochemistry, Genetics and Molecular Biology)
Next generation sequencing identifies mutations in Atonal homolog 7 (ATOH7) in families with global eye developmental defectsKhan, K., Logan, C. V., McKibbin, M., Sheridan, E., Elçioglu, N. H., Yenice, O., Parry, D. A., Fernandez-Fuentes, N., Abdelhamed, Z. I. A., Al-Maskari, A., Poulter, J. A., Mohamed, M. D., Carr, I. M., Morgan, J. E., Jafri, H., Raashid, Y., Taylor, G. R., Johnson, C. A., Inglehearn, C. F., Toomes, C. & Ali, M. 2012 In : Human Molecular Genetics.21, 4, p. 776-7838 p.
Homozygous mutations in PXDN cause congenital cataract, corneal opacity, and developmental glaucomaKhan, K., Rudkin, A., Parry, D. A., Burdon, K. P., McKibbin, M., Logan, C. V., Abdelhamed, Z. I. A., Muecke, J. S., Fernandez-Fuentes, N., Laurie, K. J., Shires, M., Fogarty, R., Carr, I. M., Poulter, J. A., Morgan, J. E., Mohamed, M. D., Jafri, H., Raashid, Y., Meng, N., Piseth, H., Toomes, C., Casson, R. J., Taylor, G. R., Hammerton, M., Sheridan, E., Johnson, C. A., Inglehearn, C. F., Craig, J. E. & Ali, M. 2011 In : American Journal of Human Genetics.89, 3, p. 464-7310 p.
Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagramsSegura, J., Jones, P. F. & Fernandez-Fuentes, N. 2011 In : BMC Bioinformatics.12, p. 352
PCRPi-DB: a database of computationally annotated hot spots in protein interfacesSegura, J. & Fernandez-Fuentes, N. 2011 In : Nucleic Acids Research.39, Database issue, p. D755-60
CAPS-DB: a structural classification of helix-capping motifsSegura, J., Oliva, B. & Fernandez-Fuentes, N. 2011 In : Nucleic Acids Research.40, D1, p. D479-D485
A mutation in the mitochondrial fission gene Dnm1l leads to cardiomyopathyAshrafian, H., Docherty, L., Leo, V., Towlson, C., Neilan, M., Steeples, V., Lygate, C. A., Hough, T., Townsend, S., Williams, D., Wells, S., Norris, D., Glyn-Jones, S., Land, J., Barbaric, I., Lalanne, Z., Denny, P., Szumska, D., Bhattacharya, S., Griffin, J. L., Hargreaves, I., Fernandez-Fuentes, N., Cheeseman, M., Watkins, H. & Dear, T. N. 2010 In : PLoS Genetics.6, 6, p. e1001000
Homozygous FOXE3 mutations cause non-syndromic, bilateral, total sclerocornea, aphakia, microphthalmia and optic disc colobomaAli, M., Buentello-Volante, B., McKibbin, M., Rocha-Medina, J. A., Fernandez-Fuentes, N., Koga-Nakamura, W., Ashiq, A., Khan, K., Booth, A. P., Williams, G., Raashid, Y., Jafri, H., Rice, A., Inglehearn, C. F. & Zenteno, J. C. 2010 In : Molecular Vision.16, p. 1162-87 p.
Structural characteristics of novel protein foldsFernandez-Fuentes, N., Dybas, J. M. & Fiser, A. 2010 In : PLoS Computational Biology.6, 4, e1000750
Presaging critical residues in protein interfaces-web server (PCRPi-W): a web server to chart hot spots in protein interfacesSegura Mora, J., Assi, S. A. & Fernandez-Fuentes, N. 2010 In : PLoS One.5, 8, p. e12352
Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancerBowers, S. R., Calero-Nieto, F. J., Valeaux, S., Fernandez-Fuentes, N. & Cockerill, P. N. 2010 In : Nucleic Acids Research.38, 18, p. 6124-3411 p.
PCRPi, Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfacesAssi, S. A., Tanaka, T., Rabbitts, T. H. & Fernandez-Fuentes, N. 2010 In : Nucleic Acids Research.38, 6, e86
Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenitaGrozdanov, P. N., Fernandez-Fuentes, N., Fiser, A. & Meier, U. T. 2009 In : Human Molecular Genetics.18, 23, p. 4546-516 p.
Evolutionary and biophysical relationships among the papillomavirus E2 proteinsBlakaj, D. M., Fernandez-Fuentes, N., Chen, Z., Hegde, R., Fiser, A., Burk, R. D. & Brenowitz, M. 2009 In : BioScience.14, p. 900-1718 p.
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB)Hermoso, A., Espadaler, J., Enrique Querol, E., Aviles, F. X., Sternberg, M. J. E., Oliva, B. & Fernandez-Fuentes, N. 2007 In : Bioinformatics and Biology Insights.1, p. 77-9014 p.
Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivityTorres, M., Fernandez-Fuentes, N., Fiser, A. & Casadevall, A. 2007 In : PLoS One.2, 12, p. e1310
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignmentsFernandez-Fuentes, N., Rai, B. K., Madrid-Aliste, C. J., Fajardo, J. E. & Fiser, A. 2007 In : Bioinformatics.23, 19, p. 2558-658 p.
M4T, a comparative protein structure modeling serverFernandez-Fuentes, N., Madrid-Aliste, C. J., Rai, B. K., Fajardo, J. E. & Fiser, A. 2007 In : Nucleic Acids Research.35, Web Server issue, p. W363-86 p.
The immunoglobulin heavy chain constant region affects kinetic and thermodynamic parameters of antibody variable region interactions with antigenTorres, M., Fernández-Fuentes, N., Fiser, A. & Casadevall, A. 2007 In : Journal of Biological Chemistry.282, 18, p. 13917-2711 p.
Saturating representation of loop conformational fragments in structure databanksFernandez-Fuentes, N. & Fiser, A. 2006 In : BMC Structural Biology.6, 15, p. 15 3488
ArchPRED: a template based loop structure prediction serverFernandez-Fuentes, N., Zhai, J. & Fiser, A. 2006 In : Nucleic Acids Research.34, Web Server issue, p. W173-W1764 p.
Insights into the mechanism of microtubule stabilization by TaxolXiao, H., Verdier-Pinard, P., Fernandez-Fuentes, N., Burd, B., Angeletti, R., Fiser, A., Horwitz, S. B. & Orr, G. A. 2006 In : Proceedings of the National Academy of Sciences of the United States of America.103, 27, p. 10166-738 p.
A supersecondary structure library and search algorithm for modeling loops in protein structuresFernandez-Fuentes, N., Oliva, B. & Fiser, A. 2006 In : Nucleic Acids Research.34, 7, p. 2085-209713 p.
Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loopsFernandez-Fuentes, N., Querol, E., Aviles, F. X., Sternberg, M. J. E. & Oliva, B. 2005 In : Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics.60, 4, p. 746-75712 p.
Classification of common functional loops of kinase super-familiesFernandez-Fuentes, N., Hermoso, A., Espadaler, J., Querol, E., Aviles, F. X. & Oliva, B. 2004 In : Proteins: Structure, Function and Genetics.56, 3, p. 539-55517 p.
ArchDB: automated protein loop classification as a tool for structural genomicsEspadaler, J., Fernandez-Fuentes, N., Hermoso, A., Querol, E., Aviles, F. X., Sternberg, M. J. E. & Oliva, B. 2004 In : Nucleic Acids Research.32, Suppl. 1, p. D185-D188
Automated detection of remote homologyDietmann, S., Fernandez-Fuentes, N. & Holm, L. 2002 In : Current Opinion in Structural Biology.12, 3, p. 362-76 p.