Publications

Maintained as a Zotero bibliography list

2021

  1. Nikolaivits Ε., Siaperas R., Agrafiotis Α., Ouazzani J., Magoulas A., Gioti A., and Topakas E., 2021. Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus. Science of the Total Environment, 775, 145818. https://doi.org/10.1016/j.scitotenv.2021.145818


2020

  1. Gioti Α., Siaperas R., Nikolaivits E., Le Goff G., Ouazzani J., Kotoulas G., & Topakas E., 2020. Draft genome sequence of a Cladosporium species isolated from the mesophotic ascidian Didemnum maculosum. Microbiology Resource Announcements (ASM) 9 (18) e00311-20. https://doi.org/10.1128/MRA.00311-20
  2. Zafeiropoulos, H., Viet, H.Q., Vasileiadou, K., Potirakis, A., Arvanitidis, C., Topalis, P., Pavloudi, C., Pafilis, E. (2020). PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. GigaScience, 2020 9:3: giaa022. https://doi.org/10.1093/gigascience/giaa022
  3. Danis, T., Tsakogiannis, A., Kristoffersen, J. B., Golani, D., Tsaparis, D., Kasapidis, P., … Manousaki, T. 2020. Building a high-quality reference genome assembly for the eastern Mediterranean Sea invasive sprinter Lagocephalus sceleratus (Tetraodontiformes, Tetraodontidae). BioRxiv, 2020.02.17.952580. https://doi.org/10.1101/2020.02.17.952580

2019

  1. Natsidis, P., Tsakogiannis, A., Pavlidis, P., Tsigenopoulos, C.S., Manousaki, T., 2019. Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. Commun Biol 2, 1–10. https://doi.org/10.1038/s42003-019-0654-5
    Preprint also available: Natsidis, P., Tsakogiannis, A., Pavlidis, P., Tsigenopoulos, C.S., Manousaki, T., 2019. Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. bioRxiv preprint 746115. https://doi.org/10.1101/746115
  2. Zafeiropoulos, H., Viet, H.Q., Vasileiadou, K., Potirakis, A., Arvanitidis, C., Topalis, P., Pavloudi, C., Pafilis, E., 2019. PEMA: from the raw .fastq files of 16S rRNA and COI marker genes to the (M)OTU-table, a thorough metabarcoding analysis. bioRxiv preprint 709113. https://doi.org/10.1101/709113
  3. Kyriakis, D., Kanterakis, A., Manousaki, T., Tsakogiannis, A., Tsagris, M., Tsamardinos, I., Papaharisis, L., Chatziplis, D., Potamias, G., Tsigenopoulos, C.S., 2019. Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing. Front Genet 10. https://doi.org/10.3389/fgene.2019.00675


2018

  1. Bounas, A., Tsaparis, D., Efrat, R., Gradev, G., Gustin, M., Mikulic, K., Rodríguez, A., Sarà, M., Kotoulas, G., Sotiropoulos, K., 2018. Genetic structure of a patchily distributed philopatric migrant: implications for management and conservation. Biol J Linn Soc 124, 633–644. https://doi.org/10.1093/biolinnean/bly073
  2. Bounas, A., Catsadorakis, G., Logotheti, A., Voslamber, B., Magoulas, A., Tsaparis, D., 2018. Conservation genetics of a resident population of Greylag Goose (Anser anser) at the southernmost limit of the species’ distribution in Europe. Avian Research 9, 47. https://doi.org/10.1186/s40657-018-0139-0
  3. Arvanitidis CD, Warwick RM, Somerfield PJ, Pavloudi C, Pafilis E, Oulas A, Chatzigeorgiou G, et al. 2018. Research Infrastructures offer capacity to address scientific questions never attempted before: Are all taxa equal? PeerJ Preprints 6:e26819v2 https://doi.org/10.7287/peerj.preprints.26819v2
  4. Christakis C.A., Polymenakou P.N., Kilias S.P., Kristoffersen J.B., Nielsen T., Nomikou P., Kotoulas G., & Magoulas A. 2018. What do I do with my metagenomes? A comparison of three online metagenomic analysis platforms, Hellenic Bioinformatics 11 – Hbio.info 2018, Thessaloniki, Greece- 15-18 November 2018. researchgate.net/publication/328392856
  5. Christakis, C. A., Polymenakou, P. N., Mandalakis, M., Nomikou, P., Kristoffersen, J. B., Lampridou, D., Kotoulas, G., and Magoulas, A. 2018. Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc. Extremophiles 22, 13–27. https://doi.org/10.1007/s00792-017-0971-x
  6. Machado, A. M., Sarropoulou, E., Castro, L. F. C., Vasconcelos, V. & Cunha, I. 2018. An important resource for understanding bio-adhesion mechanisms: Cement gland transcriptomes of two goose barnacles, Pollicipes pollicipes and Lepas anatifera (Cirripedia, Thoracica). Mar. Genomics. https://doi.org/10.1016/j.margen.2018.11.001
  7. Manousaki, T., Tsakogiannis, A., Lagnel, J., Kyriakis, D., Duncan, N., Estevez, A., Tsigenopoulos, C.S., 2018. Muscle and liver transcriptome characterization and genetic marker discovery in the farmed meagre, Argyrosomus regius. Mar Genomics 39, 39–44. https://doi.org/10.1016/j.margen.2018.01.002
  8. Tsakogiannis, A., Manousaki, T., Lagnel, J., Papanikolaou, N., Papandroulakis, N., Mylonas, C.C., Tsigenopoulos, C.S., 2018. The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics. Front Genet 9, 749. https://doi.org/10.3389/fgene.2018.00749
  9. Pauletto, M., Manousaki, T., Ferraresso, S., Babbucci, M., Tsakogiannis, A., Louro, B., Vitulo, N., Quoc, V.H., Carraro, R., Bertotto, D., Franch, R., Maroso, F., Aslam, M.L., Sonesson, A.K., Simionati, B., Malacrida, G., Cestaro, A., Caberlotto, S., Sarropoulou, E., Mylonas, C.C., Power, D.M., Patarnello, T., Canario, A.V.M., Tsigenopoulos, C., Bargelloni, L., 2018. Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish. Commun Biol 1, 1–13. https://doi.org/10.1038/s42003-018-0122-7
  10. Tsakogiannis, A., Manousaki, T., Lagnel, J., Sterioti, A., Pavlidis, M., Papandroulakis, N., Mylonas, C.C., Tsigenopoulos, C.S., 2018. The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish. Sci Rep 8, 3564. https://doi.org/10.1038/s41598-018-21992-9


2017

  1. Pavloudi C, Oulas A, Vasileiadou K, Kotoulas G, De Troch M, Friedrich MW, Arvanitidis C. 2017. Diversity and abundance of sulfate-reducing microorganisms in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) derived from dsrB gene. Aquat Microb Ecol 79:209-219. https://doi.org/10.3354/ame01829
  2. Antoniou, A., Kasapidis, P., Kotoulas, G., Mylonas, C.C., Magoulas, A., 2017. Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites. Journal of Biological Research-Thessaloniki 24, 3. https://doi.org/10.1186/s40709-017-0062-2
  3. Sarropoulou, E., Sundaram, A.Y.M., Kaitetzidou, E., Kotoulas, G., Gilfillan, G.D., Papandroulakis, N., Mylonas, C.C., Magoulas, A., 2017. Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili.Gigascience. https://doi.org/10.1093/gigascience/gix108
  4. Kaitetzidou, E., Ludwig, A., Gessner, J. & Sarropoulou, E. 2017. Expression Patterns of Atlantic Sturgeon ( Acipenser oxyrinchus ) During Embryonic Development. G3; Genes|Genomes|Genetics. https://doi.org/10.1534/g3.116.036699

2016

  1. Bravakos, P., Kotoulas, G., Skaraki, K., Pantazidou, A., Economou-Amilli, A., 2016. A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece. Molecular Phylogenetics and Evolution 98, 147–160. https://doi.org/10.1016/j.ympev.2016.02.009
  2. Pavloudi, C., Oulas, A., Vasileiadou, K., Sarropoulou, E., Kotoulas, G., Arvanitidis, C. 2016. Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea). Marine Genomics 28, 71-81. https://doi.org/10.1016/j.margen.2016.01.005
  3. Varsos C, Patkos T, Oulas A, Pavloudi C, Gougousis A, Ijaz U, Filiopoulou I, Pattakos N, Vanden Berghe E, Fernández-Guerra A, Faulwetter S, Chatzinikolaou E, Pafilis E, Bekiari C, Doerr M, Arvanitidis C 2016. Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab). Biodiversity Data Journal 4: e8357. https://doi.org/10.3897/BDJ.4.e8357
  4. Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., 2016. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 48, 427-437. https://doi.org/10.1038/ng.3526
  5. Sarropoulou, E., Tsalafouta, A., Sundaram, A.Y.M., Gilfillan, G.D., Kotoulas, G., Papandroulakis, N., Pavlidis, M., 2016. Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata). BMC Genomics 2016. https://doi.org/10.1186/s12864-016-2874-0

2015

  1. Christakis C.A., Polymenakou P.N., Mandalakis M., Oulas A., Kotoulas G., Gontikaki E., Smyrli M., Katharios P., Nomikou P., Magoulas A. 2015. Culture-dependent and culture-independent studies shed light in the prokaryotic diversity of microbes in the Kolumbo volcano and Santorini caldera, Greece. 6th Mikrobiokosmos Conference 2015 – New Horizons in the Micro World. Athens, Greece, 3-5 April 2015 researchgate.net/publication/273131887
  2. Manousaki, T., Tsakogiannis, A., Taggart, J.B., Palaiokostas, C., Tsaparis, D., Lagnel, J., Chatziplis, D., Magoulas, A., Papandroulakis, N., Mylonas, C.C., Tsigenopoulos, C.S., 2015. Exploring a Nonmodel Teleost Genome Through RAD Sequencing-Linkage Mapping in Common Pandora, Pagellus erythrinus and Comparative Genomic Analysis. G3 (Bethesda) 6, 509–519. https://doi.org/10.1534/g3.115.023432
  3. Polymenakou, P. N., Christakis, C. A., Mandalakis, M., and Oulas, A. 2015. Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea. Res. Microbiol. 166, 448–457. https://doi.org/10.1016/j.resmic.2015.03.005
  4. Kaitetzidou, E., Xiang, J., Antonopoulou, E., Tsigenopoulos, C. S. & Sarropoulou, E. 2015. Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax). Physiol. Genomics. https://doi.org/10.1152/physiolgenomics.00001.2015

2014

  1. Manousaki, T., Tsakogiannis, A., Lagnel, J., Sarropoulou, E., Xiang, J.Z., Papandroulakis, N., Mylonas, C.C., Tsigenopoulos, C.S., 2014. The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo). BMC Genomics 15. https://doi.org/10.1186/1471-2164-15-655
2013
  1. Kilias, S. P., Nomikou, P., Papanikolaou, D., Polymenakou, P. N., Godelitsas, A., Argyraki, A., Carey, S., Gamaletsos, P., Mertzimekis, T. J., Stathopoulou, E., Goettlicher, J., Steininger, R., Betzelou, K., Livanos, I., Christakis, C., Bell, K. C., and Scoullos, M. 2013. New insights into hydrothermal vent processes in the unique shallow-submarine arc-volcano, Kolumbo (Santorini), Greece. Sci. Rep. 3, 2421. http://doi.org/10.1038/srep02421

2012

  1. Sarropoulou, E., Galindo-Villegas, J., García-Alcázar, A., Kasapidis, P. & Mulero, V. Characterization of European sea bass transcripts by RNA SEQ after oral vaccine against V. anguillarum. Mar. Biotechnol. 2012. https://doi.org/10.1007/s10126-012-9466-z

prior to 2012

  1. Sarropoulou, E., Sepulcre, P., Poisa-Beiro, L., Mulero, V., Meseguer, J., Figueras, A., Novoa, B., Terzoglou, V., Reinhardt, R., & Magoulas, A. 2009. Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax. BMC Genomics, 10(1), 157. http://doi.org/10.1186/1471-2164-10-157

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