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

Segura, J, Jones, PF & Fernandez-Fuentes, N 2011, 'Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams' BMC Bioinformatics, vol 12, pp. 352. DOI: 10.1186/1471-2105-12-352
Segura, J & Fernandez-Fuentes, N 2011, 'PCRPi-DB: a database of computationally annotated hot spots in protein interfaces' Nucleic Acids Research, vol 39, no. Database issue, pp. D755-60. DOI: 10.1093/nar/gkq1068
Ashrafian, H, Docherty, L, Leo, V, Towlson, C, Neilan, M, Steeples, V, Lygate, CA, 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, JL, Hargreaves, I, Fernandez-Fuentes, N, Cheeseman, M, Watkins, H & Dear, TN 2010, 'A mutation in the mitochondrial fission gene Dnm1l leads to cardiomyopathy' PLoS Genetics, vol 6, no. 6, pp. e1001000. DOI: 10.1371/journal.pgen.1001000
Ali, M, Buentello-Volante, B, McKibbin, M, Rocha-Medina, JA, Fernandez-Fuentes, N, Koga-Nakamura, W, Ashiq, A, Khan, K, Booth, AP, Williams, G, Raashid, Y, Jafri, H, Rice, A, Inglehearn, CF & Zenteno, JC 2010, 'Homozygous FOXE3 mutations cause non-syndromic, bilateral, total sclerocornea, aphakia, microphthalmia and optic disc coloboma' Molecular Vision, vol 16, pp. 1162-8.
Fernandez-Fuentes, N, Dybas, JM & Fiser, A 2010, 'Structural characteristics of novel protein folds' PLoS Computational Biology, vol 6, no. 4, e1000750. DOI: 10.1371/journal.pcbi.1000750
Segura Mora, J, Assi, SA & 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, vol 5, no. 8, pp. e12352. DOI: 10.1371/journal.pone.0012352
Bowers, SR, Calero-Nieto, FJ, Valeaux, S, Fernandez-Fuentes, N & Cockerill, PN 2010, 'Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer' Nucleic Acids Research, vol 38, no. 18, pp. 6124-34. DOI: 10.1093/nar/gkq356
Assi, SA, Tanaka, T, Rabbitts, TH & 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, vol 38, no. 6, e86. DOI: 10.1093/nar/gkp1158
Grozdanov, PN, Fernandez-Fuentes, N, Fiser, A & Meier, UT 2009, 'Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita' Human Molecular Genetics, vol 18, no. 23, pp. 4546-51. DOI: 10.1093/hmg/ddp416
Blakaj, DM, Fernandez-Fuentes, N, Chen, Z, Hegde, R, Fiser, A, Burk, RD & Brenowitz, M 2009, 'Evolutionary and biophysical relationships among the papillomavirus E2 proteins' BioScience, vol 14, pp. 900-17. DOI: 10.2741/3285
Hermoso, A, Espadaler, J, Enrique Querol, E, Aviles, FX, Sternberg, MJE, Oliva, B & Fernandez-Fuentes, N 2007, 'Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB)' Bioinformatics and Biology Insights, vol 1, pp. 77-90.
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, vol 2, no. 12, pp. e1310. DOI: 10.1371/journal.pone.0001310
Fernandez-Fuentes, N, Rai, BK, Madrid-Aliste, CJ, Fajardo, JE & Fiser, A 2007, 'Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments' Bioinformatics, vol 23, no. 19, pp. 2558-65. DOI: 10.1093/bioinformatics/btm377
Fernandez-Fuentes, N, Madrid-Aliste, CJ, Rai, BK, Fajardo, JE & Fiser, A 2007, 'M4T, a comparative protein structure modeling server' Nucleic Acids Research, vol 35, no. Web Server issue, pp. W363-8. DOI: 10.1093/nar/gkm341
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, vol 282, no. 18, pp. 13917-27. DOI: 10.1074/jbc.M700661200
Fernandez-Fuentes, N, Zhai, J & Fiser, A 2006, 'ArchPRED: a template based loop structure prediction server' Nucleic Acids Research, vol 34, no. Web Server issue, pp. W173-W176. DOI: 10.1093/nar/gkl113
Fernandez-Fuentes, N & Fiser, A 2006, 'Saturating representation of loop conformational fragments in structure databanks' BMC Structural Biology, vol 6, no. 15, pp. 15. DOI: 10.1186/1472-6807-6-15
Xiao, H, Verdier-Pinard, P, Fernandez-Fuentes, N, Burd, B, Angeletti, R, Fiser, A, Horwitz, SB & Orr, GA 2006, 'Insights into the mechanism of microtubule stabilization by Taxol' Proceedings of the National Academy of Sciences of the United States of America, vol 103, no. 27, pp. 10166-73. DOI: 10.1073/pnas.0603704103
Fernandez-Fuentes, N, Oliva, B & Fiser, A 2006, 'A supersecondary structure library and search algorithm for modeling loops in protein structures' Nucleic Acids Research, vol 34, no. 7, pp. 2085-2097. DOI: 10.1093/nar/gkl156
Fernandez-Fuentes, N, Querol, E, Aviles, FX, Sternberg, MJE & 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, vol 60, no. 4, pp. 746-757. DOI: 10.1002/prot.20516
Fernandez-Fuentes, N, Hermoso, A, Espadaler, J, Querol, E, Aviles, FX & Oliva, B 2004, 'Classification of common functional loops of kinase super-families' Proteins: Structure, Function and Genetics, vol 56, no. 3, pp. 539-555. DOI: 10.1002/prot.20136
Espadaler, J, Fernandez-Fuentes, N, Hermoso, A, Querol, E, Aviles, FX, Sternberg, MJE & Oliva, B 2004, 'ArchDB: automated protein loop classification as a tool for structural genomics' Nucleic Acids Research, vol 32, no. Suppl. 1, pp. D185-D188. DOI: 10.1093/nar/gkh002
Dietmann, S, Fernandez-Fuentes, N & Holm, L 2002, 'Automated detection of remote homology' Current Opinion in Structural Biology, vol 12, no. 3, pp. 362-7. DOI: 10.1016/S0959-440X(02)00332-9
Oyama, LB, Girdwood, SE, Cookson, AR, Fernandez-fuentes, N, Privé, F, Vallin, HE, Wilkinson, TJ, Golyshin, PN, Golyshina, OV, Mikut, R, Hilpert, K, Richards, J, Wootton, M, Edwards, JE, Maresca, M, Perrier, J, Lundy, FT, Luo, Y, Zhou, M, Hess, M, Mantovani, HC, Creevey, CJ & Huws, SA 2017, 'The rumen microbiome: an underexplored resource for novel antimicrobial discovery' npj Biofilms and Microbiomes, vol 3, no. 1, 33. DOI: 10.1038/s41522-017-0042-1
Oyama, LB, Crochet, J-A, Edwards, JE, Girdwood, S, Cookson, A, Fernandez-Fuentes, N, Hilpert, K, Golyshin, PN, Golyshina, OV, Privé, F, Hess, M, Mantovani, HC, Creevey, C & Huws, S 2017, 'Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis' Frontiers in Chemistry, vol 5, 51. DOI: 10.3389/fchem.2017.00051
Garcia-Garcia, J, Valls-Comamala, V, Guney, E, Andreu, D, Muñoz , FJ, Fernandez-Fuentes, N & Oliva, B 2017, 'iFrag: A Protein-Protein Interface Prediction Server Based on Sequence Fragments' Journal of Molecular Biology. DOI: 10.1016/j.jmb.2016.11.034
Marín-López, MA, Planas-Iglesias, J, Aguiree-Plans, J, Bonet, J, Garcia-Garcia, J, Fernandez-Fuentes, N & Oliva, B 2017, 'On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures' Bioinformatics.
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, vol 32, no. 21, pp. 3339-3341. DOI: 10.1093/bioinformatics/btw403
Bouraoui, H, Desrousseaux, M-L, Ioannou, E, Alvira, P, Manaï, M, Rémond, C, Dumon, C, Fernandez-Fuentes, N & O'Donohue, MJ 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, vol 9, 140. DOI: 10.1186/s13068-016-0550-x
Poglayen, D, Marín-López, MA, 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, vol 44, no. 3, pp. 917-924. DOI: 10.1042/BST20150001
Chalmers, IW, Fitzsimmons, CM, Brown, M, Pierrot, C, Jones, FM, Wawrzyniak, JM, Fernandez-Fuentes, N, Tukahebwa, EM, Dunne, DW, Khalife, J & Hoffmann, KF 2015, 'Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment' PLoS Neglected Tropical Diseases, vol 9, no. 7, pp. e0003920. DOI: 10.1371/journal.pntd.0003920
Segura, J, Marín-López, MA, Jones, PF, Oliva, B, Fernandez-fuentes, N & Keskin, O (ed.) 2015, 'VORFFIP-Driven Dock: V-D2OCK, a Fast and Accurate Protein Docking Strategy' PLoS One, vol 10, no. 3, e0118107. DOI: 10.1371/journal.pone.0118107
Kara, A, Vickers, M, Swain, M, Whitworth, DE & Fernandez-Fuentes, N 2015, 'Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor' BMC Bioinformatics, vol 16, no. 1, 297. DOI: 10.1186/s12859-015-0741-7
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, vol 30, no. 13, pp. 1935-1936. DOI: 10.1093/bioinformatics/btu129
Sewell, H, Tanaka, T, Omari, KE, Mancini, EJ, Cruz, A, Fernandez-Fuentes, N, Chambers, J & Rabbitts, TH 2014, 'Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex' Scientific Reports, vol 4, 3643. DOI: 10.1038/srep03643
Bonet, J, Planas-Iglesias, J, Garcia-Garcia, J, Marín-López, MA, Fernandez-Fuentes, N & Oliva, B 2014, 'ArchDB 2014: Structural classification of loops in proteins' Nucleic Acids Research, vol 42, no. D1, pp. D315-D319. DOI: 10.1093/nar/gkt1189
Cruz-Migoni, A, Fernandez-Fuentes, N & Rabbitts, TH 2013, 'Peptides: minimal drug surrogates to interrogate and interfere with protein function' MedChemComm, vol 4, pp. 1218-1221. DOI: 10.1039/C3MD00142C
Fernandez-Fuentes, N & Fiser, A 2013, A modular perspective of protein structures: application to fragment based loop modeling. in AE Kister (ed.), Protein Supersecondary Structures. vol. 932, Methods in Molecular Biology, vol. 932, Springer Nature, pp. 141-158. DOI: 10.1007/978-1-62703-065-6_9
Segura, J, Jones, PF & Fernandez-Fuentes, N 2012, 'A holistic in silico approach to predict functional sites in protein structures' Bioinformatics, vol 28, no. 14, pp. 1845-1850. DOI: 10.1093/bioinformatics/bts269
Segura, J, Blas Pastor, JR & 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. Chapter 19 edn, Biochemistry, Genetics and Molecular Biology, InTechOpen, pp. 379-404. DOI: 10.5772/37268
Khan, K, Logan, CV, McKibbin, M, Sheridan, E, Elçioglu, NH, Yenice, O, Parry, DA, Fernandez-Fuentes, N, Abdelhamed, ZIA, Al-Maskari, A, Poulter, JA, Mohamed, MD, Carr, IM, Morgan, JE, Jafri, H, Raashid, Y, Taylor, GR, Johnson, CA, Inglehearn, CF, 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, vol 21, no. 4, pp. 776-783. DOI: 10.1093/hmg/ddr509
Segura, J, Oliva, B & Fernandez-Fuentes, N 2011, 'CAPS-DB: a structural classification of helix-capping motifs' Nucleic Acids Research, vol 40, no. D1, pp. D479-D485. DOI: 10.1093/nar/gkr879
Khan, K, Rudkin, A, Parry, DA, Burdon, KP, McKibbin, M, Logan, CV, Abdelhamed, ZIA, Muecke, JS, Fernandez-Fuentes, N, Laurie, KJ, Shires, M, Fogarty, R, Carr, IM, Poulter, JA, Morgan, JE, Mohamed, MD, Jafri, H, Raashid, Y, Meng, N, Piseth, H, Toomes, C, Casson, RJ, Taylor, GR, Hammerton, M, Sheridan, E, Johnson, CA, Inglehearn, CF, Craig, JE & Ali, M 2011, 'Homozygous mutations in PXDN cause congenital cataract, corneal opacity, and developmental glaucoma' American Journal of Human Genetics, vol 89, no. 3, pp. 464-73. DOI: 10.1016/j.ajhg.2011.08.005