• Martínez-González B, and 25 Coauthors (including Llorens C and Soriano B). 2022. SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes. Microbiol Spectr. 
  • Martinez-Gonzalez B, and 18 coauthors (Including Llorens C and Soriano B). 2022. Vaccine-breakthrough infections with SARS-CoV-2 Alpha mirror mutations in Delta Plus, Iota and Omicron. J Clin Invest.
  • Hafez A and 17 co-authors (including Soriano B, Ceprian R, Elsayed. AA, Martinez-Sanchis G, and Llorens C). 2022. RNASeq and VariantSeq applications and Server Side of GPRO suite. ArXiv
  • Amanatidou AI and 21 Coauthors including Llorens C). 2022.Association of Dietary Patterns with MRI Markers of Hepatic Inflammation and Fibrosis in the MAST4HEALTH Study. Int. J. Environ. Res. Public Health 19(2), 971
  • Gomez-Gonzalez A, Zamora I, Soriano B, Llorens C. 2022. Prototipo de servidor web para el análisis bioinformático de datos de citometría de flujo. BiBi Software Article: 2022-SOFT1, ISSN 1988-7957.
  • Navarrete-Muñoz MA, Llorens C, Benito JM, Rallon N. 2022. Extracellular Vesicles as a New Promising Therapy in HIV Infection. Front. Immunol., 04 January 2022.
  • 2021

  • Soriano B, Kuprovic M, Llorens C. ICTV Report Consortium. 2021. ICTV Virus Taxonomy Profile: Belpaoviridae 2021.Journal of General Virology,102-11.
  • Baquero F, Campos M, Llorens C, Sempere JM. 2021. P systems in the time of COVID-19. J. Membr. Comput. doi:
  • Campos M, Sempere JM, Galán JC, Moya A, Llorens C, de-los-Angeles C, Baquero-Artigao F, Cantón R, Baquero F. 2021. Simulating the impact of non-pharmaceutical interventions limiting transmission in COVID-19 epidemics using a membrane computing model, microLife, Volume 2, 2021, uqab011. doi:
  • Herreros-Pomares A, Llorens C, Soriano B, Zhang F, Gallach S, Bagan L, Murillo J, Jantus-Lewintre E, Bagan J. 2021. Oral microbiome in Proliferative Verrucous Leukoplakia exhibits loss of diversity and enrichment of pathogens, Oral Oncology, Volume 120,105404.doi:
  • Arastehfar A, (and 12 coauthors including Hafez A). 2021.Clonal Candidemia Outbreak by Candida parapsilosis Carrying Y132F in Turkey: Evolution of a Persisting Challenge. Front Cell Infect Microbiol;11:676177.doi:
  • Arcos SC (and 14 coauthors including Llorens C). 2021.Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae. Microorganisms 9(5):1088.doi:
  • Kanoni S (and 29 co-authors including Llorens C). 2021. Nutrigenetic Interactions Might Modulate the Antioxidant and Anti-Inflammatory Status in Mastiha-Supplemented Patients With NAFLD. Frontiers in Immunology, 12, 1688 doi:
  • Trilla-Fuertes L, Gámez-Pozo A, Maurel J. (and 19 coauthors, includind Llorens C). 2021. Description of the genetic variants identified in a cohort of patients diagnosed with localized anal squamous cell carcinoma and treated with panitumumab. Sci Rep 11, 7402 doi:
  • Llorens C, Soriano B, Navarrete-Muñoz MA, Hafez A, Arnau V, Benito JM, Gabaldon T, Rallon N, Perez-Sanchez J, Kropovic M. 2021.Reverse-transcribing viruses of the families Metaviridae, Belpaoviridae and Pseudoviridae (order Ortervirales). In: Bamford, D.H. and Zuckerman, M. (eds.) Encyclopedia of Virology, 4th Edition, vol. 3, pp. 653-666. Oxford: Academic Press. Elsevier, doi:
  • Pérez-Sánchez R, Carnero-Morán Á, Soriano B, Llorens C, Oleaga A. 2021. RNA-seq analysis and gene expression dynamics in the salivary glands of the argasid tick Ornithodoros erraticus along the trophogonic cycle. Parasites Vectors 14, 170.
  • Herreros-Pomares A, Llorens C, Soriano B, Bagan L, Moreno A, Calabuig-Fariñas S, Jantus-Lewintre E, Bagan J. 2021. Differentially methylated genes in proliferative verrucous leukoplakia reveal potential malignant biomarkers for oral squamous cell carcinoma, Oral Oncology, Volume 116,105191
  • Amerikanou C and 32 coauthors (including Soriano B, Llorens C and Roig FJ). 2021.Effect of Mastiha supplementation on NAFLD: The MAST4HEALTH Randomised, Controlled Trial. Mol Nutr Food Res. Feb 24:e2001178. Epub ahead of print. PMID: 33629536.
  • Oleaga A, Soriano B, Llorens C, Pérez-Sánchez R. 2021. Sialotranscriptomics of the argasid tick Ornithodoros moubata along the trophogonic cycle. PLOS Neglected Tropical Diseases 15(2): e0009105.
  • Llorens C, Soriano B, Kuprovic M, ICTV Report Consortium. 2021. ICTV Virus Taxonomy Profile: Pseudoviridae. Journal of General Virology,102-3
  • 2020

  • Hafez A, Futami R, Arastehfar A, Daneshnia F, Miguel A, Roig FJ, Soriano B, Perez-Sánchez J, Boekhout T, Gabaldón T, Llorens C. 2020.SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files, Bioinformatics, 37(11), 1610-1612
  • Llorens C, Soriano B, Kuprovic M, ICTV Report Consortium. 2020.ICTV Virus Taxonomy Profile: Metaviridae. Journal of General Virology, 101-11
  • Llorens C, Soriano B, Trilla-Fuertes L, Bagan L, Ramos-Ruis R, Gamez-Pozo A, Peña C, Bagan JV. 2020. Immune expression profile identification in a group of proliferative verrucous leukoplakia patients: a pre-cancer niche for oral squamous cell carcinoma development. Clin Oral Invest.
  • Arastehfar A, and 18 co-authors (Including Hafez A). 2020. Recent increase in the prevalence of fluconazole-non-susceptible Candida tropicalis blood isolates in Turkey: Clinical implication of azole-non-susceptible and fluconazole tolerant phenotypes and genotyping. Frontiers in Microbiology.
  • Megri Y, Arastehfar A, Boekhout T, and 7 coauthors (including Hafez A.). 2020.Candida tropicalis is the most prevalent yeast species causing candidemia in Algeria: the urgent need for antifungal stewardship and infection control measures. Antimicrob Resist Infect Control 9, 50.
  • Arastehfar A, Daneshnia F, Hafez A and 13 co-authors. 2020. Antifungal susceptibility, genotyping, resistance mechanism, and clinical profile of Candida tropicalis blood isolates, Medical Mycology, Volume 58, Issue 6,Pages 766–773,
  • Díaz R, Sandoval P, Rodrigues-Diez RR, del Peso G, Jiménez-Heffernan JA, Ramos-Ruíz R, Llorens C, Laham G, Alvarez-Quiroga M, López-Cabrera M, Ruiz-Ortega M, Bajo M.A, Selgas R. 2020. Increased miR-7641 Levels in Peritoneal Hyalinizing Vasculopathy in Long-Term Peritoneal Dialysis Patients. Int. J. Mol. Sci. 21 5824.
  • Trilla-Fuertes L, Ramos-Ruiz R, Blanca-Lopez N, Lopez-Camacho E, Martin-Pedraza L, Ryan Murua P, Diaz-Almiron M, Llorens C, Gabaldon T, Moya A, Fresno JA, Gamez-Pozo A. 2020. Functional characterization of SARS-CoV-2 infection suggests a complex inflammatory response and metabolic alterations. BioRxiv
  • Campos M, San Millan A, Sempere JM, Lanza VF, Coque TM, Llorens C, Baquero F. 2020.Simulating the Influence of Conjugative Plasmids Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model. Antimicrobial Agents and Chemotherapy May 2020, AAC.00593-20
  • Trilla-Fuertes L (and 23 Co-authors including Llorens C and Gamez A). 2020.Comprehensive Characterization of the Mutational Landscape in Localized Anal Squamous Cell Carcinoma. Translational Oncology.
  • Trilla-Fuertes L (and 23 Co-authors including Llorens C and Gamez A). 2020.Genetic profile and functional proteomics of anal squamous cell carcinoma: proposal for a molecular classification. Mol Cell Proteomics 19(4): 690-700
  • Hovhannisyan H, Hafez A, Llorens C, Gabaldon T. 2020.CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies. Bioinformatics. 36(3): 925-927
  • 2019

  • Fouad MM, Hafez A, Hassanien AE. 2019. Optimizing topologies in wireless sensor networks: A comparative analysis between the Grey Wolves and the Chicken Swarm Optimization algorithms. Computer Networks 163, 106882.
  • Pérez-Sánchez J, Naya-Català F, Soriano B, Piazzon MA, Hafez A, Gabaldón T, Llorens C, Sitjà-Bobadilla A, Calduch-Giner J. 2019.Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream. Front. Mar. Sci. 20
  • OPATHY Consortium (including Hafez A, and Llorens C), Gabaldon T. 2019.Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS microbiology reviews.43(5); 517–547'Aguilar-Duran L, Figuereido R, Seminago R, Roig FJ, Llorens C, Valmaseda-Castellon E. F. 2019.A metagenomic study of patients with alveolar osteitis after tooth extraction. A preliminary case-control study. Clinical Oral Investigations, 1-10
  • Campos M, Capilla R, Llorens C, Canton R, Moya A, Sempere JM, Coque T, Fernandez-Lanza V, Naya F, Futami R, Baquero F. 2019.Simulating multilevel dynamics of antimicrobial Resistance in a membrane computing Model. MBio 10(1),e02460-18
  • 2018

  • Rodríguez-García E, Olagüe C, Ríus-Rocabert S, Ferrero R, Llorens C, Larrea E, Fortes P, Prieto J, González-Aseguinolaza G, Nistal-Villan E.2018TMEM173 Alternative Spliced Isoforms Modulate Viral Replication through the STING Pathway. ImmunoHorizons, 2,11 pp 363-376.
  • Garcia-Jimenez P, Llorens C, Roig FJ, Robina RR.2018Analysis of the Transcriptome of the Red Seaweed Grateloupia imbricata with Emphasis on Reproductive Potential. Marine Drugs, 16,490.
  • Baquero F, Campos M, Llorens C, Sempere JM. 2018A Model of Antibiotic Resistance Evolution Dynamics Through P Systems with Active Membranes and Communication Rules. Enjoying Natural Computing pp 33-34.'Llorens C, Arcos SC, Robertson L, Ramos R, Futami R, Soriano B, Ciordia S, Careche M, González-Muñoz M, Jiménez-Ruiz Y, Carballeda-Sangiao N, Moneo I, Albar JP, Blaxter M and Navas A. 2018.Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns. BMC Genomics 19:592.
  • Herrera M, Llorens C, Rodríguez M, Herrera A, Ramos R, Gil B, Candia A, Larriba MJ, Garre P, Earl J, Rodríguez-Garrote M, Caldés T, Bonilla F, Carrato A, García-Barberán V and Peña C. 2018.Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colorectal cancer. Molecular Cancer, 17:114
  • Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski N, Pappu HR, Pooggin M, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon S, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH. 2018.Ortervirales: A new viral order unifying five families of reverse-transcribing viruses. Journal of Virology. 92:12 5 e00515-18
  • Saus E, Willis JR, Pryszcz LP, Hafez A, Llorens C, Himmelbauer H, Gabaldon T. 2018.nextPARS: Parallel probing of RNA structures in Illumina. Published in Advance January 22, 2018, RNAdoi: 10.1261/rna.063073.117
  • Roig F, Gonzalez-Candelas F, Sanjuan E, Feil E, Fouz B, Llorens C, Baker-Austin C, Oliver J, Danin-Poleg Y, Gibas C, Kashi Y, Gulig PA, Morrison SS, Amaro C. 2018.Phylogeny of Vibrio vulnificus from the analysis of the core-genome: implications for intra-species taxonomy. Front. Microbiol. 8, 2613;doi: 10.3389/fmicb.2017.02613
  • 2017

  • Unver T, Wu Z, Sterck L, Turktas M, Lohaus R, Li Z, Yang M, He L, Deng T, Escalante FJ, Llorens C, Roig FJ, Parmaksiz I, Dundar E, Xie F, Zhang B, Ipek A, Uranbey S, Erayman M, Ilhan E, Badad O, Ghazal H, Lightfoot DA, Kasarla P, Colantonio V, Tombologlu H, Hernandez P, Mete N, Cetin O, Van Montagu M, Yang H, Gao Q, Dorado G, and Van de Peer Y. 2017.Genome of wild olive and the evolution of oil biosynthesis Proc. Natl. Acad. Sci. USA. 2017, 114, 44: E9413-E9422,doi:10.1073/pnas.1708621114.
  • Ramirez M, Velázquez R, López-Piñeiro A, Naranjo B, Roig F and Llorens C. 2017. New Insights into the Genome Organization of Yeast Killer Viruses Based on “Atypical” Killer Strains Characterized by High-Throughput Sequencing.Toxins 9(9), 292; doi:10.3390/toxins9090292
  • Cortés-Acha B, Figueiredo R, Seminago R, Roig FJ, Llorens C, Valmaseda-Castellón E. 2017. Microbiota Analysis of Biofilms on Experimental Abutments Mimicking Dental Implants: An in Vivo Model. Journal of Periodontology 01-20 :doi:10.1902/jop.2017.170051
  • 2016

  • Berlanga M, Llorens C, Comas J, Guerrero R. 2016. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana.PLoS ONE 11(4): e0152400. doi:10.1371/journal.pone.0152400
  • 2015

  • Campos M, Llorens C, Sempere JM, Futami R, Rodríguez I, Carrasco P, Capilla R, Latorre A, Coque TM, Moya A AND Baquero F. 2015. A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES).Biology Direct 2015, 10:41.
  • Berlanga M, LLorens C, Umeneta J, Guerrero-Moreno R. 2015. Metagenómica y filogenia de los tapetes microbianos del Parque Natural de La Camarga (Delta del Ródano, Francia). En Avances en Microbiologia, Elena González Fandos, Universidad de la Rioja (ed. lit.),ISBN 978-84-606-8181-6, pág. 188 href='
  • 2014

  • Lysøe E, Harris LJ, Walkowiak S, Subramaniam R, Divon HH, Riiser ES, Llorens C, Gabaldón T, Kistler HH, Jonkers W, Kolseth AK, Nielsen KF, Thrane U, and Frandsen RJN. 2014. The Genome of the Generalist Plant Pathogen Fusarium avenaceum Is Enriched with Genes Involved in Redox, Signaling and Secondary Metabolism.PLoS ONE 9(11): e112703. doi:10.1371/journal.pone.0112703
  • 2013

  • Carmona bayonas A, Luengo Gil G, Fong Puig CA, Llorens C. 2013. Los elementos geneticos moviles en la celula tumoral: El despertar de un gigante.REVISTA EUBACTERIA (NOVIEMBRE 2013) Nº32 / ISSN-1697-0071
  • 2012

  • Llorens C, Bernet GP, Ramasamy S, Feschotte C, Moya A 2012. On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain.Mobile Genetic Elements 2(5), September-October-2012.
  • 2011

  • Bernet GP, Muñoz-Pomer A, Dominguez-Escriba L, Covelli L, Bernad L, Ramasamy S, Futami R, Sempere JM, Moya A AND Llorens C. 2011. GyDB Mobilomics: LTR retroelements and integrase-related transposons of the Pea aphid Acyrthosiphon pisum genome.Mobile Genetic Elements 1(2), 0-1. 1-7-2011. Landes Bioscience.
  • Covelli L, Muñoz-Pomer A, Dominguez-Escriba L, Futami R, Bernet GP, Moya A and Llorens C. 2011. The GyDB collection is now publicly available within the Gypsy Database of Mobile Genetic Elements. Biotechvana bioinformatics:2011-CR1
  • Muñoz-Pomer A, Futami R, Sempere JM, Moya A, and Llorens C. 2011. CheckAlign 2.0.Biotechvana Bioinformatics: 2011-SOFT1.
  • Muñoz-Pomer A, Futami R, Covelli L, Domínguez-Escribà L, Bernet GP, Sempere JM, Moya A, and Llorens C. 2011. TIME: a sequence editor for the molecular analysis of large DNA and protein sequence samples.Biotechvana Bioinformatics: 2011-SOFT2.
  • Futami R, Muñoz-Pomer A, Viu JM, Dominguez-Escribá L, Covelli L, Bernet GP, Sempere JM, Moya A, Llorens C. GPRO: the professional tool for management, functional analysis and annotation of omic sequences and databases (2011)Biotechvana Bioinformatics: 2011-SOFT3
  • Llorens C, Futami R, Covelli L, Dominguez-Escriba L, Viu JM, Tamarit D, Aguilar-Rodríguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, and Moya A. 2011. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061
  • 2010

  • THE INTERNATIONAL APHID GENOMICS CONSORTIUM (including Llorens C and Futami R). 2010 . Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol, 8(2):e1000313 DOI / ISBN:10.1371/journal.pbio.1000313
  • 2009

  • Llorens C, Muñoz-Pomer A, Bernad L, Botella H, and Moya A. 2009. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees.Biology Direct, 4:41
  • Llorens C, Futami R, Renaud G, and Moya A. 2009. Bioinformatic Flowchart and Database to Investigate the Origins and Diversity of Clan AA Peptidases.Biology Direct, 4:3
  • Llorens C, Muñoz-Pomer A, Futami R, and Moya A. 2009. The GyDB Collection of Viral and Mobile Genetic Element Models.In Biotechvana Bioinformatics, CR: GyDB collection V2
  • 2008

  • Llorens C, Futami R, Bezemer D and Moya A. 2008. The Gypsy Database (GyDB) of mobile genetic elements.Nucleic Acids Research (NAR) 36 (Database Issue):38-46
  • Llorens C, Fares MA, and Moya A. 2008. Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis.BMC Evolutionary Biology, 8:276
  • Llorens C, Futami R, Muñoz-Pomer A, Vicente-Ripolles M, and Moya A. 2008. Introducing Biotechvana Bioinformatics.In Biotechvana Bioinformatics, Intro
  • Llorens C, Futami R, Vicente-Ripollés M, and Moya A. 2008. The CheckAlign logo-maker application in analyses of both gapped and ungapped DNA and protein alignments.In Biotechvana Bioinformatics, SOFT:CheckAlign
  • Llorens C, Futami R, Vicente-Ripollés M, and Moya A. 2008. Phylograph: A multifunction java editor for handling phylogenetic trees.In Biotechvana Bioinformatics, SOFT: Phylograph
  • Llorens C, Futami R, and Moya A. 2008. The GyDB collection: Ty3/Gypsy and Retroviridae LTR retroelements and related nonviral proteins.In Biotechvana Bioinformatics, CR:GyDB collection
  • Futami R, Llorens C, Vicente-Ripollés M, and Moya A. 2008. The GyDB Package 1.0.In Biotechvana Bioinformatics, DU: GyDB Package
  • Llorens C, Vicente-Ripollés M, and Moya A. 2008. The Join Alignments Server version 1.0.In Biotechvana Bioinformatics, SCR:JAS
  • Llorens C, Vicente-Ripollés M, and Moya A. 2008. The Alignment Format Converter Server 1.0In Biotechvana Bioinformatics SCR: AFC
  • Llorens C, Futami R, Vicente-Ripolles M, and Moya A. 2008. Biotechvana Search Engine 1.0.In Biotechvana Bioinformatics DU:BSE
  • Futami R, Llorens C, and Moya A. 2008. Biotechvana Queue Manager 1.0.In Biotechvana Bioinformatics, DU:BQM
  • Llorens C, Vicente-Ripollés M, and Moya A. 2008. RMXSC server 1.0.In Biotechvana Bioinformatics, SCR: RMXSC
  • 2001

  • Llorens C and Marin I. 2001. A mammalian gene evolved from the Integrase domain of an LTR-retrotransposon.Molecular Biology and Evolution. 18 (8): 1597-1600
  • 2000

  • Marin I and Llorens C. 2000. 'Ty3/Gypsy Retrotransposons: Description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data'.Molecular Biology and Evolution. 17(7): 1040-1049

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