Profile
Postdoctoral Fellow.
Untangling the complexity of gene regulatory networks in prokaryotes. Artificial intelligence enthusiast.
Publications
Fernandez, Leyden; Bertilsson, Stefan; Peura, Sari
Non-cyanobacterial diazotrophs dominate nitrogen-fixing communities in permafrost thaw ponds Journal Article
In: Limnology and Oceanography, vol. 65, pp. S180–S193, 2020.
@article{fernandez2020non,
title = {Non-cyanobacterial diazotrophs dominate nitrogen-fixing communities in permafrost thaw ponds},
author = {Leyden Fernandez and Stefan Bertilsson and Sari Peura},
year = {2020},
date = {2020-01-01},
journal = {Limnology and Oceanography},
volume = {65},
pages = {S180--S193},
publisher = {John Wiley & Sons, Inc. Hoboken, USA},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernandez, Leyden; Peura, Sari; Eiler, Alexander; Linz, Alexandra M; McMahon, Katherine D; Bertilsson, Stefan
Diazotroph genomes and their seasonal dynamics in a stratified humic bog lake Journal Article
In: Frontiers in microbiology, vol. 11, pp. 1500, 2020.
@article{fernandez2020diazotroph,
title = {Diazotroph genomes and their seasonal dynamics in a stratified humic bog lake},
author = {Leyden Fernandez and Sari Peura and Alexander Eiler and Alexandra M Linz and Katherine D McMahon and Stefan Bertilsson},
year = {2020},
date = {2020-01-01},
journal = {Frontiers in microbiology},
volume = {11},
pages = {1500},
publisher = {Frontiers},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Buck, Moritz; Garcia, Sarahi L; Vidal, Leyden Fernandez; Martin, Gaetan; Rodriguez, Gustavo Martinez A; Saarenheimo, Jatta; Zopfi, Jakob; Bertilsson, Stefan; Peura, Sari
Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds Journal Article
In: bioRxiv, 2020.
@article{buck2020comprehensive,
title = {Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds},
author = {Moritz Buck and Sarahi L Garcia and Leyden Fernandez Vidal and Gaetan Martin and Gustavo Martinez A Rodriguez and Jatta Saarenheimo and Jakob Zopfi and Stefan Bertilsson and Sari Peura},
year = {2020},
date = {2020-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernandez-Vidal, Leyden
Non-cyanobacterial nitrogen fixation insights in humic freshwater lakes and ponds PhD Thesis
Acta Universitatis Upsaliensis, 2019.
@phdthesis{fernandez2019non,
title = {Non-cyanobacterial nitrogen fixation insights in humic freshwater lakes and ponds},
author = {Leyden Fernandez-Vidal},
year = {2019},
date = {2019-01-01},
school = {Acta Universitatis Upsaliensis},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}
Eiler, Alexander; Mondav, Rhiannon; Sinclair, Lucas; Fernandez-Vidal, Leyden; Scofield, Douglas G; Schwientek, Patrick; Martinez-Garcia, Manuel; Torrents, David; McMahon, Katherine D; Andersson, Siv GE; others,
Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria Journal Article
In: The ISME journal, vol. 10, no. 8, pp. 1902–1914, 2016.
@article{eiler2016tuning,
title = {Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria},
author = {Alexander Eiler and Rhiannon Mondav and Lucas Sinclair and Leyden Fernandez-Vidal and Douglas G Scofield and Patrick Schwientek and Manuel Martinez-Garcia and David Torrents and Katherine D McMahon and Siv GE Andersson and others},
year = {2016},
date = {2016-01-01},
journal = {The ISME journal},
volume = {10},
number = {8},
pages = {1902--1914},
publisher = {Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Vidal, Leyden Fernández; others,
Papel de las regiones reguladoras de la expresión génica en la adaptación a factores ambientales en procariotas PhD Thesis
Universitat de Barcelona, 2015.
@phdthesis{fernandez2015papel,
title = {Papel de las regiones reguladoras de la expresión génica en la adaptación a factores ambientales en procariotas},
author = {Leyden Fernández Vidal and others},
year = {2015},
date = {2015-01-01},
school = {Universitat de Barcelona},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}
Fernandez, Leyden; Mercader, Josep M; Planas-F`elix, Merc`e; Torrents, David
Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities Journal Article
In: BMC genomics, vol. 15, no. 1, pp. 1–12, 2014.
@article{fernandez2014adaptation,
title = {Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities},
author = {Leyden Fernandez and Josep M Mercader and Merc{`e} Planas-F{`e}lix and David Torrents},
year = {2014},
date = {2014-01-01},
journal = {BMC genomics},
volume = {15},
number = {1},
pages = {1--12},
publisher = {BioMed Central},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rossi, Daniela; Pedrali, Alice; Urbano, Mariangela; Gaggeri, Raffaella; Serra, Massimo; Fernández, Leyden; Fernández, Michael; Caballero, Julio; Ronsisvalle, Simone; Prezzavento, Orazio; others,
Identification of a potent and selective $sigma$1 receptor agonist potentiating NGF-induced neurite outgrowth in PC12 cells Journal Article
In: Bioorganic & medicinal chemistry, vol. 19, no. 21, pp. 6210–6224, 2011.
@article{rossi2011identification,
title = {Identification of a potent and selective $sigma$1 receptor agonist potentiating NGF-induced neurite outgrowth in PC12 cells},
author = {Daniela Rossi and Alice Pedrali and Mariangela Urbano and Raffaella Gaggeri and Massimo Serra and Leyden Fernández and Michael Fernández and Julio Caballero and Simone Ronsisvalle and Orazio Prezzavento and others},
year = {2011},
date = {2011-01-01},
journal = {Bioorganic & medicinal chemistry},
volume = {19},
number = {21},
pages = {6210--6224},
publisher = {Pergamon},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernandez, Michael; Caballero, Julio; Fernandez, Leyden; Sarai, Akinori
Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM) Journal Article
In: Molecular diversity, vol. 15, no. 1, pp. 269–289, 2011.
@article{fernandez2011genetic,
title = {Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM)},
author = {Michael Fernandez and Julio Caballero and Leyden Fernandez and Akinori Sarai},
year = {2011},
date = {2011-01-01},
journal = {Molecular diversity},
volume = {15},
number = {1},
pages = {269--289},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernandez, Michael; Caballero, Julio; Fernandez, Leyden; Sarai, Akinori
Graphical Representations of Protein Sequences for Alignment-Free Comparative and Predictive Studies. Recognition of Protease Inhibition Pattern from H-Depleted Molecular Graph Representation of Protease Sequences Journal Article
In: Current Bioinformatics, vol. 5, no. 4, pp. 241–252, 2010.
@article{fernandez2010graphical,
title = {Graphical Representations of Protein Sequences for Alignment-Free Comparative and Predictive Studies. Recognition of Protease Inhibition Pattern from H-Depleted Molecular Graph Representation of Protease Sequences},
author = {Michael Fernandez and Julio Caballero and Leyden Fernandez and Akinori Sarai},
year = {2010},
date = {2010-01-01},
journal = {Current Bioinformatics},
volume = {5},
number = {4},
pages = {241--252},
publisher = {Bentham Science Publishers},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lazo, Yoslandy; Suárez, Laureano; Fernández, Michael; Fernández, Leyden
Modeling of lattice parameters of the $gamma$ and $gamma$′ phases of the superalloys with base nickel by using a multiple linear regression analysis Journal Article
In: Superlattices and Microstructures, vol. 45, no. 3, pp. 117–124, 2009.
@article{lazo2009modeling,
title = {Modeling of lattice parameters of the $gamma$ and $gamma$′ phases of the superalloys with base nickel by using a multiple linear regression analysis},
author = {Yoslandy Lazo and Laureano Suárez and Michael Fernández and Leyden Fernández},
year = {2009},
date = {2009-01-01},
journal = {Superlattices and Microstructures},
volume = {45},
number = {3},
pages = {117--124},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Michael; Fernández, Leyden; Abreu, Jose Ignacio; Garriga, Miguel
Classification of voltage-gated K+ ion channels from 3D pseudo-folding graph representation of protein sequences using genetic algorithm-optimized support vector machines Journal Article
In: Journal of Molecular Graphics and Modelling, vol. 26, no. 8, pp. 1306–1314, 2008.
@article{fernandez2008classification,
title = {Classification of voltage-gated K+ ion channels from 3D pseudo-folding graph representation of protein sequences using genetic algorithm-optimized support vector machines},
author = {Michael Fernández and Leyden Fernández and Jose Ignacio Abreu and Miguel Garriga},
year = {2008},
date = {2008-01-01},
journal = {Journal of Molecular Graphics and Modelling},
volume = {26},
number = {8},
pages = {1306--1314},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Michael; Fernández, Leyden; Caballero, Julio; Abreu, José Ignacio; Reyes, Grethel
Proteochemometric Modeling of the Inhibition Complexes of Matrix Metalloproteinases with N-Hydroxy-2-[(Phenylsulfonyl) Amino] Acetamide Derivatives Using Topological Autocorrelation Interaction Matrix and Model Ensemble Averaging Journal Article
In: Chemical biology & drug design, vol. 72, no. 1, pp. 65–78, 2008.
@article{fernandez2008proteochemometric,
title = {Proteochemometric Modeling of the Inhibition Complexes of Matrix Metalloproteinases with N-Hydroxy-2-[(Phenylsulfonyl) Amino] Acetamide Derivatives Using Topological Autocorrelation Interaction Matrix and Model Ensemble Averaging},
author = {Michael Fernández and Leyden Fernández and Julio Caballero and José Ignacio Abreu and Grethel Reyes},
year = {2008},
date = {2008-01-01},
journal = {Chemical biology & drug design},
volume = {72},
number = {1},
pages = {65--78},
publisher = {Blackwell Publishing Ltd Oxford, UK},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Michael; Caballero, Julio; Fernández, Leyden; Abreu, Jose Ignacio; Acosta, Gianco
Classification of conformational stability of protein mutants from 3D pseudo-folding graph representation of protein sequences using support vector machines Journal Article
In: Proteins: Structure, Function, and Bioinformatics, vol. 70, no. 1, pp. 167–175, 2008.
@article{fernandez2008classificationb,
title = {Classification of conformational stability of protein mutants from 3D pseudo-folding graph representation of protein sequences using support vector machines},
author = {Michael Fernández and Julio Caballero and Leyden Fernández and Jose Ignacio Abreu and Gianco Acosta},
year = {2008},
date = {2008-01-01},
journal = {Proteins: Structure, Function, and Bioinformatics},
volume = {70},
number = {1},
pages = {167--175},
publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernandez, Michael; Fernandez, Leyden; Sanchez, Pedro; Caballero, Julio; Abreu, Jose Ignacio
Proteometric modelling of protein conformational stability using amino acid sequence autocorrelation vectors and genetic algorithm-optimised support vector machines Journal Article
In: Molecular Simulation, vol. 34, no. 9, pp. 857–872, 2008.
@article{fernandez2008proteometric,
title = {Proteometric modelling of protein conformational stability using amino acid sequence autocorrelation vectors and genetic algorithm-optimised support vector machines},
author = {Michael Fernandez and Leyden Fernandez and Pedro Sanchez and Julio Caballero and Jose Ignacio Abreu},
year = {2008},
date = {2008-01-01},
journal = {Molecular Simulation},
volume = {34},
number = {9},
pages = {857--872},
publisher = {Taylor & Francis},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Michael; Caballero, Julio; Fernández, Leyden; Abreu, José Ignacio; Garriga, Miguel
Protein radial distribution function (P-RDF) and Bayesian-Regularized Genetic Neural Networks for modeling protein conformational stability: Chymotrypsin inhibitor 2 mutants Journal Article
In: Journal of Molecular Graphics and Modelling, vol. 26, no. 4, pp. 748–759, 2007.
@article{fernandez2007protein,
title = {Protein radial distribution function (P-RDF) and Bayesian-Regularized Genetic Neural Networks for modeling protein conformational stability: Chymotrypsin inhibitor 2 mutants},
author = {Michael Fernández and Julio Caballero and Leyden Fernández and José Ignacio Abreu and Miguel Garriga},
year = {2007},
date = {2007-01-01},
journal = {Journal of Molecular Graphics and Modelling},
volume = {26},
number = {4},
pages = {748--759},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Caballero, Julio; Fernández, Leyden; Garriga, Miguel; Abreu, José Ignacio; Collina, Simona; Fernández, Michael
Proteometric study of ghrelin receptor function variations upon mutations using amino acid sequence autocorrelation vectors and genetic algorithm-based least square support vector machines Journal Article
In: Journal of Molecular Graphics and Modelling, vol. 26, no. 1, pp. 166–178, 2007.
@article{caballero2007proteometric,
title = {Proteometric study of ghrelin receptor function variations upon mutations using amino acid sequence autocorrelation vectors and genetic algorithm-based least square support vector machines},
author = {Julio Caballero and Leyden Fernández and Miguel Garriga and José Ignacio Abreu and Simona Collina and Michael Fernández},
year = {2007},
date = {2007-01-01},
journal = {Journal of Molecular Graphics and Modelling},
volume = {26},
number = {1},
pages = {166--178},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Michael; Abreu, José Ignacio; Caballero, Julio; Garriga, Miguel; Fernández, Leyden
Comparative modeling of the conformational stability of chymotrypsin inhibitor 2 protein mutants using amino acid sequence autocorrelation (AASA) and amino acid 3D autocorrelation (AA3DA) vectors and ensembles of Bayesian-regularized genetic neural networks Journal Article
In: Molecular Simulation, vol. 33, no. 13, pp. 1045–1056, 2007.
@article{fernandez2007comparative,
title = {Comparative modeling of the conformational stability of chymotrypsin inhibitor 2 protein mutants using amino acid sequence autocorrelation (AASA) and amino acid 3D autocorrelation (AA3DA) vectors and ensembles of Bayesian-regularized genetic neural networks},
author = {Michael Fernández and José Ignacio Abreu and Julio Caballero and Miguel Garriga and Leyden Fernández},
year = {2007},
date = {2007-01-01},
journal = {Molecular Simulation},
volume = {33},
number = {13},
pages = {1045--1056},
publisher = {Taylor & Francis},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Leyden; Caballero, Julio; Abreu, José Ignacio; Fernández, Michael
Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: Gene V protein mutants Journal Article
In: Proteins: Structure, Function, and Bioinformatics, vol. 67, no. 4, pp. 834–852, 2007.
@article{fernandez2007amino,
title = {Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: Gene V protein mutants},
author = {Leyden Fernández and Julio Caballero and José Ignacio Abreu and Michael Fernández},
year = {2007},
date = {2007-01-01},
journal = {Proteins: Structure, Function, and Bioinformatics},
volume = {67},
number = {4},
pages = {834--852},
publisher = {Wiley Subscription Services, Inc., A Wiley Company Hoboken},
keywords = {},
pubstate = {published},
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}
Caballero, Julio; Fernandez, Leyden; Abreu, Jose Ignacio; Fernández, Michael
Amino Acid Sequence Autocorrelation vectors and ensembles of Bayesian-Regularized Genetic Neural Networks for prediction of conformational stability of human lysozyme mutants Journal Article
In: Journal of chemical information and modeling, vol. 46, no. 3, pp. 1255–1268, 2006.
@article{caballero2006amino,
title = {Amino Acid Sequence Autocorrelation vectors and ensembles of Bayesian-Regularized Genetic Neural Networks for prediction of conformational stability of human lysozyme mutants},
author = {Julio Caballero and Leyden Fernandez and Jose Ignacio Abreu and Michael Fernández},
year = {2006},
date = {2006-01-01},
journal = {Journal of chemical information and modeling},
volume = {46},
number = {3},
pages = {1255--1268},
publisher = {American Chemical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hernández, Karel; Fernández, Leyden; Gómez, Leissy; Villalonga, Reynaldo
Glycosidation of trypsin with end-group activated dextran Journal Article
In: Process Biochemistry, vol. 41, no. 5, pp. 1155–1159, 2006.
@article{hernandez2006glycosidation,
title = {Glycosidation of trypsin with end-group activated dextran},
author = {Karel Hernández and Leyden Fernández and Leissy Gómez and Reynaldo Villalonga},
year = {2006},
date = {2006-01-01},
journal = {Process Biochemistry},
volume = {41},
number = {5},
pages = {1155--1159},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Leyden; Gómez, Leissy; Ram'irez, Héctor L; Villalonga, Maria L; Villalonga, Reynaldo
Thermal stabilization of trypsin with glycol chitosan Journal Article
In: Journal of Molecular Catalysis B: Enzymatic, vol. 34, no. 1-6, pp. 14–17, 2005.
@article{fernandez2005thermal,
title = {Thermal stabilization of trypsin with glycol chitosan},
author = {Leyden Fernández and Leissy Gómez and Héctor L Ram{'i}rez and Maria L Villalonga and Reynaldo Villalonga},
year = {2005},
date = {2005-01-01},
journal = {Journal of Molecular Catalysis B: Enzymatic},
volume = {34},
number = {1-6},
pages = {14--17},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Villalonga, Maria L; Reyes, Gretel; Fragoso, Alex; Cao, Roberto; Fernández, Leyden; Villalonga, Reynaldo
Chemical glycosidation of trypsin with O-carboxymethyl-poly-$beta$-cyclodextrin: catalytic and stability properties Journal Article
In: Biotechnology and applied biochemistry, vol. 41, no. 3, pp. 217–223, 2005.
@article{villalonga2005chemical,
title = {Chemical glycosidation of trypsin with O-carboxymethyl-poly-$beta$-cyclodextrin: catalytic and stability properties},
author = {Maria L Villalonga and Gretel Reyes and Alex Fragoso and Roberto Cao and Leyden Fernández and Reynaldo Villalonga},
year = {2005},
date = {2005-01-01},
journal = {Biotechnology and applied biochemistry},
volume = {41},
number = {3},
pages = {217--223},
publisher = {Blackwell Publishing Ltd Oxford, UK},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Michael; Caballero, Julio; Fernández, Leyden; Sánchez, Pedro
Modeling Protein Conformational Stability Using Amino Acid Sequence Autocorrelation Vectors and RBF Neural Networks Journal Article
In: 0000.
@article{fernandezmodeling,
title = {Modeling Protein Conformational Stability Using Amino Acid Sequence Autocorrelation Vectors and RBF Neural Networks},
author = {Michael Fernández and Julio Caballero and Leyden Fernández and Pedro Sánchez},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fernández, Michael; Caballero, Julio; Fernández, Leyden; Abreu, José Ignacio
Amino Acid Sequence Autocorrelation vectors and ensembles of Bayesian-Regularized Genetic Neural Networks for prediction of conformational stability of protein mutants Journal Article
In: 0000.
@article{fernandezamino,
title = {Amino Acid Sequence Autocorrelation vectors and ensembles of Bayesian-Regularized Genetic Neural Networks for prediction of conformational stability of protein mutants},
author = {Michael Fernández and Julio Caballero and Leyden Fernández and José Ignacio Abreu},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Leyden Fernandez is currently affiliated with IceLab. She is working in close collaboration with the Department of Molecular Biology and a multidisciplinary team with expertise in molecular and clinical infection biology. Leyden graduated from Havana University, Cuba with a bachelor and master degree in Biochemistry. She then moved to Spain to do a PhD in biomedical informatics at Barcelona Supercomputing Center. Afterwards, Leyden did a second PhD in microbial ecology at Uppsala University followed by a short postdoc in stem cell biology at Karolinska Institute.
Leyden’s main project at IceLab aims to identify bacterial determinants that can be explored as targets for new antimicrobials. Antibiotic-resistant infections are challenging modern medicine approaches. The overuse of antibiotics to treat chronic infections is exacerbating this problem. Broad spectrum antibiotics also affect human microbial flora, a natural barrier that prevents colonization by exogenous microorganisms. Leyden will use transcriptomic data from pathogenic bacteria to model complex gene regulatory networks. Subsequently, relevant information about adaptation mechanisms in pathogenic bacteria will be extracted and evaluated as potential targets for new antimicrobials.
Current Projects
New targets for future antimicrobials (Kempe Foundation)
M Fallman, K. Avican, M Rosvall, J. Normark
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