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

2017

Oyama, L.B., Crochet, J., 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. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis. Frontiers in Chemistry 5 51 10.3389/fchem.2017.00051 Cadair

Garcia-Garcia, J., Valls-Comamala, V., Guney, E., Andreu, D., Muñoz, F.J., Fernandez-Fuentes, N., Oliva, B. 2017. iFrag: A Protein-Protein Interface Prediction Server Based on Sequence Fragments. Journal of Molecular Biology 10.1016/j.jmb.2016.11.034 Cadair

Marín-López, M.A., Planas-Iglesias, J., Aguiree-Plans, J., Bonet, J., Garcia-Garcia, J., Fernandez-Fuentes, .., Oliva, B. 2017. On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. Bioinformatics

2016

Kara, A., Vickers, M., Swain, M., Whitworth, D., Fernandez-Fuentes, N. 2016. MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins. Bioinformatics 32 (21) pp. 3339-3341. 10.1093/bioinformatics/btw403 Cadair

Bouraoui, H., Desrousseaux, M., Ioannou, E., Alvira, P., Manaï, M., Rémond,, C., Dumon, C., Fernandez-Fuentes, N., O'Donohue, M.J. 2016. The GH51 α-l-arabinofuranosidase from Paenibacillus sp. THS1 is multifunctional, hydrolyzing main-chain and side-chain glycosidic bonds in heteroxylans. Biotechnology for Biofuels 9 140 10.1186/s13068-016-0550-x Cadair

Poglayen, D., Marín-López, M.A., Bonet, J., Fornes, O., Garcia-Garcia, J., Planas-Iglesias, J., Segura, J., Oliva, B., Fernandez-Fuentes, N. 2016. InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research. Biochemical Society Transactions 44 (3) pp. 917-924. 10.1042/BST20150001 Cadair

2015

Chalmers, 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. Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment. PLoS Neglected Tropical Diseases 9 (7) pp. e0003920. 10.1371/journal.pntd.0003920 Cadair

Segura, J., Marín-López, M.A., Jones, P.F., Oliva, B., Fernandez-fuentes, N.Keskin, O. 2015. VORFFIP-Driven Dock: V-D2OCK, a Fast and Accurate Protein Docking Strategy. PLoS One 10 (3) e0118107 10.1371/journal.pone.0118107 Cadair

Kara, A., Vickers, M., Swain, M., Whitworth, D.E., Fernandez-Fuentes, N. 2015. Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. BMC Bioinformatics 16 (1) 297 10.1186/s12859-015-0741-7 Cadair

2014

Bonet, J., Segura, J., Planas-Iglesias, J., Oliva, B., Fernandez-Fuentes, N. 2014. Frag’r’Us: Knowledge-based sampling of protein backbone conformations for de novo structure-based protein design. Bioinformatics 30 (13) pp. 1935-1936. 10.1093/bioinformatics/btu129 Cadair

Sewell, H., Tanaka, T., Omari, K.E., Mancini, E.J., Cruz, A., Fernandez-Fuentes, N., Chambers, J., Rabbitts, T.H. 2014. Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex. Scientific Reports 4 3643 10.1038/srep03643 Other Cadair

Bonet, J., Planas-Iglesias, J., Garcia-Garcia, J., Marín-López, M.A., Fernandez-Fuentes, N., Oliva, B. 2014. ArchDB 2014: Structural classification of loops in proteins. Nucleic Acids Research 42 (D1) pp. D315-D319. 10.1093/nar/gkt1189 Other Cadair

2013

Cruz-Migoni, A., Fernandez-Fuentes, N., Rabbitts, T.H. 2013. Peptides: minimal drug surrogates to interrogate and interfere with protein function. MedChemComm 4 pp. 1218-1221. 10.1039/C3MD00142C Cadair

Fernandez-Fuentes, N., Fiser, A. 2013. A modular perspective of protein structures: application to fragment based loop modeling. In A. E. Kister. (ed) Protein Supersecondary Structures. Methods in Molecular Biology, vol. 932 Springer Nature pp. 141-158. 10.1007/978-1-62703-065-6_9 Cadair

2012

Segura, J., Jones, P.F., Fernandez-Fuentes, N. 2012. A holistic in silico approach to predict functional sites in protein structures. Bioinformatics 28 (14) pp. 1845-1850. 10.1093/bioinformatics/bts269 Cadair

Segura, J., Blas Pastor, J.R., Fernandez-Fuentes, N. 2012. Computational Tools and Databases for the Study and Characterization of Protein Interactions. In W. Cai., H. Hong. (eds) Protein-Protein Interactions - Computational and Experimental Tools. Biochemistry, Genetics and Molecular Biology Chapter 19th edn, InTechOpen pp. 379-404. 10.5772/37268 Cadair

Khan, 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. Next generation sequencing identifies mutations in Atonal homolog 7 (ATOH7) in families with global eye developmental defects. Human Molecular Genetics 21 (4) pp. 776-783. 10.1093/hmg/ddr509 Cadair

2011

Segura, J., Fernandez-Fuentes, N. 2011. PCRPi-DB: a database of computationally annotated hot spots in protein interfaces. Nucleic Acids Research 39 (Database issue) pp. D755-60. 10.1093/nar/gkq1068 Cadair

Segura, J., Oliva, B., Fernandez-Fuentes, N. 2011. CAPS-DB: a structural classification of helix-capping motifs. Nucleic Acids Research 40 (D1) pp. D479-D485. 10.1093/nar/gkr879 Cadair

Khan, 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. Homozygous mutations in PXDN cause congenital cataract, corneal opacity, and developmental glaucoma. American Journal of Human Genetics 89 (3) pp. 464-73. 10.1016/j.ajhg.2011.08.005 Cadair

Segura, J., Jones, P.F., Fernandez-Fuentes, N. 2011. Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams. BMC Bioinformatics 12 pp. 352. 10.1186/1471-2105-12-352 Cadair

2010

Ashrafian, 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. A mutation in the mitochondrial fission gene Dnm1l leads to cardiomyopathy. PLoS Genetics 6 (6) pp. e1001000. 10.1371/journal.pgen.1001000 Cadair

Ali, 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. Homozygous FOXE3 mutations cause non-syndromic, bilateral, total sclerocornea, aphakia, microphthalmia and optic disc coloboma. Molecular Vision 16 pp. 1162-8. Cadair

Fernandez-Fuentes, N., Dybas, J.M., Fiser, A. 2010. Structural characteristics of novel protein folds. PLoS Computational Biology 6 (4) e1000750 10.1371/journal.pcbi.1000750 Cadair

Segura Mora, J., Assi, S.A., Fernandez-Fuentes, N. 2010. Presaging critical residues in protein interfaces-web server (PCRPi-W): a web server to chart hot spots in protein interfaces. PLoS One 5 (8) pp. e12352. 10.1371/journal.pone.0012352 Cadair

Bowers, S.R., Calero-Nieto, F.J., Valeaux, S., Fernandez-Fuentes, N., Cockerill, P.N. 2010. Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer. Nucleic Acids Research 38 (18) pp. 6124-34. 10.1093/nar/gkq356 Cadair

Assi, S.A., Tanaka, T., Rabbitts, T.H., Fernandez-Fuentes, N. 2010. PCRPi, Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces. Nucleic Acids Research 38 (6) e86 10.1093/nar/gkp1158 Cadair

2009

Grozdanov, P.N., Fernandez-Fuentes, N., Fiser, A., Meier, U.T. 2009. Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita. Human Molecular Genetics 18 (23) pp. 4546-51. 10.1093/hmg/ddp416 Cadair

Blakaj, D.M., Fernandez-Fuentes, N., Chen, Z., Hegde, R., Fiser, A., Burk, R.D., Brenowitz, M. 2009. Evolutionary and biophysical relationships among the papillomavirus E2 proteins. BioScience 14 pp. 900-17. 10.2741/3285 Cadair

2007

Hermoso, A., Espadaler, J., Enrique Querol, E., Aviles, F.X., Sternberg, M.J.E., Oliva, B., Fernandez-Fuentes, N. 2007. Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB). Bioinformatics and Biology Insights 1 pp. 77-90. Cadair

Torres, M., Fernandez-Fuentes, N., Fiser, A., Casadevall, A. 2007. Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivity. PLoS One 2 (12) pp. e1310. 10.1371/journal.pone.0001310 Cadair

Fernandez-Fuentes, N., Rai, B.K., Madrid-Aliste, C.J., Fajardo, J.E., Fiser, A. 2007. Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics 23 (19) pp. 2558-65. 10.1093/bioinformatics/btm377 Cadair

Fernandez-Fuentes, N., Madrid-Aliste, C.J., Rai, B.K., Fajardo, J.E., Fiser, A. 2007. M4T, a comparative protein structure modeling server. Nucleic Acids Research 35 (Web Server issue) pp. W363-8. 10.1093/nar/gkm341 Cadair

Torres, M., Fernández-Fuentes, N., Fiser, A., Casadevall, A. 2007. The immunoglobulin heavy chain constant region affects kinetic and thermodynamic parameters of antibody variable region interactions with antigen. Journal of Biological Chemistry 282 (18) pp. 13917-27. 10.1074/jbc.M700661200 Cadair

2006

Fernandez-Fuentes, N., Zhai, J., Fiser, A. 2006. ArchPRED:a template based loop structure prediction server. Nucleic Acids Research 34 (Web Server issue) pp. W173-6. 10.1093/nar/gkl113 Cadair

Fernandez-Fuentes, N., Fiser, A. 2006. Saturating representation of loop conformational fragments in structure databanks. BMC Structural Biology 6 (15) pp. 15. 10.1186/1472-6807-6-15 Cadair

Xiao, H., Verdier-Pinard, P., Fernandez-Fuentes, N., Burd, B., Angeletti, R., Fiser, A., Horwitz, S.B., Orr, G.A. 2006. Insights into the mechanism of microtubule stabilization by Taxol. Proceedings of the National Academy of Sciences of the United States of America 103 (27) pp. 10166-73. 10.1073/pnas.0603704103 Cadair

Fernandez-Fuentes, N., Oliva, B., Fiser, A. 2006. A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Research 34 (7) pp. 2085-97. 10.1093/nar/gkl156 Cadair

2005

Fernandez-Fuentes, N., Querol, E., Aviles, F.X., Sternberg, M.j.E., Oliva, B. 2005. Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 60 (4) pp. 746-757. 10.1002/prot.20516 Cadair

2004

Espadaler, J., Fernandez-Fuentes, N., Hermoso, A., Querol, E., Aviles, F.X., Sternberg, M.J.E., Oliva, B. 2004. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Research 32 (Suppl. 1) pp. D185-D188. 10.1093/nar/gkh002 Cadair

Fernandez-Fuentes, N., Hermoso, A., Espadaler, J., Querol, E., Aviles, F.X., Oliva, B. 2004. Classification of common functional loops of kinase super-families. Proteins: Structure, Function and Genetics 56 (3) pp. 539-555. 10.1002/prot.20136 Cadair

2002

Dietmann, S., Fernandez-Fuentes, N., Holm, L. 2002. Automated detection of remote homology. Current Opinion in Structural Biology 12 (3) pp. 362-7. 10.1016/S0959-440X(02)00332-9 Cadair