I am Christina

Welcome to my site!

Publications

These are my publications!

Journal articles:

2024

  • Hug LA, Hatzenpichler R, Moraru C, Soares A, Meyer F, Heyder A, The Data Reuse Consortium, Probst AJ (2024). A roadmap for fair reuse of public microbiome data. Nature Microbiology. Submitted - Under review
  • Pagalilauan Α, Pavloudi C, Ospina SM, Smith A, Saw J (2024) Interaction with refuse piles drives co-occurrence of core gut microbiota in workers of the ant Aphaenogaster picea. Access Microbiology. doi: 10.1099/acmi.0.000832.v1. Submitted - Under review
  • Daraghmeh N, Exter K, Pagnier J, …., Pavloudi C, Obst M (2024) A long-term ecological research data set from the marine genetic monitoring programme ARMS-MBON 2018-2020. Molecular Ecology Resources. Submitted - Under review
  • Pavloudi C, Shlafstein MD, De La Flor YT, Smith EM, Peñuela AC, Papke E, Slattery K, Lissner G, Oliver L, Coelho LC, Oline DK, Videau P, Strangman WK, Ushijima B, Saw JH (2024) Janthinobacterium aestuarii sp. nov., a novel violacein-producing bacterium isolated from water samples near monuments in Washington DC, USA. International Journal of Systematic and Evolutionary Microbiology. Submitted - Under review (corresponding author)
  • Cecchetto M, Dettai A, Gallut C, Obst M, Kuklinski P Balazy P, Chelchowski M, Małachowicz M, Poćwierz-Kotus A, Zbawicka M, Reiss H, Eléaume MP, Ficetola GF, Pavloudi C, Exter K, Schiaparelli S (2024) Seasonality of primary production, rather than its magnitude, explains the richness of pioneer hard-bottom animals at the global scale. Nature Communications. Submitted - Under review
  • Skliros D, Kostakou M, Kokari C, Tsertou MI, Pavloudi C, Zafeiropoulos H, Katharios P, Flemetakis E (2023) Unveiling emerging opportunistic fish pathogens in aquaculture: A comprehensive seasonal study of microbial composition in Mediterranean fish hatcheries. FEMS Microbiology Ecology. Submitted - Under review
  • Skaraki K, Pavloudi C, Dailianis T, Lagnel J, Pantazidou A, Magoulas A, Kotoulas G (2024) Microbial diversity in four Mediterranean irciniid sponges. Biodiversity Data Journal. 12: e114809, doi: 10.3897/BDJ.12.e114809 (corresponding author)
  • Vasileiadou K, Chatzinikolaou E, Klayn S, Pavloudi C , Reizopoulou S (2024) Editorial: ‘Marine Biodiversity Hotspots-Challenges and Resilience’. Frontiers in Marine Science 11:1338242, doi: 10.3389/fmars.2024.1338242
  • Shaw CG, Pavloudi C , Crow RS, Saw JH, Smith LC (2024) Spotting disease disrupts the microbiome of infected Strongylocentrotus purpuratus sea urchins. BMC Microbiology 24(11), doi: 10.1186/s12866-023-03161-9

2023

  • Sarafidou G, Tsaparis D, Issaris Y, Chatzigeorgiou G, Grigoriou P, Chatzinikolaou E, Pavloudi C (2023) Insights on Pinna nobilis genetic connectivity in the Eastern Mediterranean Sea. PeerJ 11:e16491, doi: 10.7717/peerj.16491
  • Zafeiropoulos H, Beracochea M, Ninidakis S, Exter K, Potirakis A, De Moro G, Richardson L, Corre E, Machado J, Pafilis E, Santi I, Kotoulas G, Finn RD, Cox C, Pavloudi C (2023) metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data. Gigascience 12: giad078, doi: 10.1093/gigascience/giad078
  • Shaw C, Pavloudi C, Barela-Hudgell M, Crow R, Saw J, Pyron A, Smith LC (2023) Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium. Pathogens and Disease. Pathogens and Disease 81:1-14, doi: 10.1093/femspd/ftad025
  • Bilbao J, Pavloudi C, Blanco-Rayón E, Franco J, Madariaga I, Seoane S (2023) Phytoplankton community composition in relation to environmental variability in the Urdaibai estuary (SE Bay of Biscay): Microscopy and eDNA metabarcoding. Marine Environmental Research. doi: 10.1016/j.marenvres.2023.106175
  • Santi I, Beluche O, Beraud M, Buttigieg PL, Casotti R, Cox CJ, Cunliffe M, Davies N, De Cerio OD, Exter K, Kervella AE, Kotoulas G, Lagaisse R, Laroquette A, Louro B, Not F, Obst M, Pavloudi C, Poulain J, Præbel K, Vanaverbeke J, Pade N (2023) European Marine Omics Biodiversity Observation Network: a strategic outline for the implementation of omics approaches in ocean observation. Frontiers in Marine Science.Frontiers in Marine Science 10:1118120, doi: 10.3389/fmars.2023.1118120
  • Leff RT, MacDougall J, Pavloudi C, Oliver L, Slattery K, Lissner G, Saw JH (2023) Draft genome sequences of three bacterial species from aquatic habitats near Washington, DC. Microbiology Resource Announcements e01319-22, doi: 10.1128/mra.01319-22
  • Pavloudi C, Tsertou MI, Antonopoulou E, Katharios P (2023) Investigation of Systemic Granulomatosis in cultured meagre, Argyrosomus regius, using clinical metagenomics. Aquaculture 567:739249, doi: 10.1016/j.aquaculture.2023.739249

2022

  • Pavloudi C, Zafeiropoulos H (2022) Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community. FEMS Microbiology Ecology 98(12): 1-18, doi: 10.1093/femsec/fiac141 (corresponding author)
  • Paragkamian S, Sarafidou G, Mavraki D, Pavloudi C, Beja J, Eliezer M, Lipizer M, Boicenco L, Vandepitte L, Perez-Perez R, Zafeiropoulos H, Arvanitidis C, Pafilis E, Gerovasileiou V (2022) Automating the curation process of historical literature on marine biodiversity using text mining: the DECO workflow. Frontiers in Marine Science 9:940844, doi: 10.3389/fmars.2022.940844
  • Grau A, Villalba A, Navas JI, Hansjosten B, Cruz JMV, Garcia March JR, Prado P, Follana G, Morage T, Vázquez-Luis M, Álvarez E, Katharios P, Pavloudi C, et al. (2022) Wide-geographic and long-term analysis of the role of pathogens in the decline of Pinna nobilis to critically endangered species. Frontiers in Marine Science 9, doi: 10.3389/fmars.2022.666640

2021

  • Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. doi: 10.3897/mbmg.5.69657
  • Samuel RM, Meyer R, Buttigieg PL, Davies N, Jeffery NW, Meyer C, Pavloudi C, Pitz KJ, Sweetlove M, Theroux S, van de Kamp J, Watts A (2021) Towards a Global Public Repository of Community Protocols to encourage Best Practices in Biomolecular Ocean Observing and Research. Frontiers in Marine Science 8:758694. doi: 10.3389/fmars.2021.758694
  • Keklikoglou Κ, Arvanitidis C, Chatzigeorgiou G, Chatzinikolaou E, Karagiannidis E, Koletsa T, Magoulas A, Makris K, Mavrothalassitis G, Papanagnou E-D, Papazoglou AS, Pavloudi C, et al. (2021) Micro-CT for biological and biomedical studies: a comparison of imaging techniques. Journal of Imaging. Journal of Imaging, 7(9): 172, doi: 10.3390/jimaging7090172
  • Nikolopoulou S, Berov D, Klayn S, Dimitrov L, Velkovsky K, Chatzinikolaou E, Chatzigeorgiou G, Karamfilov V, Pavloudi C (2021) Benthic habitat mapping of Plazh Gradina – Zlatna ribka (Black Sea) and Karpathos and Saria islands (Mediterranean Sea). Biodiversity Data Journal, 9: e71972, doi: 10.3897/BDJ.9.e71972 (corresponding author)
  • Zafeiropoulos H, Gioti A, Ninidakis S, Potirakis A, Paragkamian S, Angelova N, Antoniou A, Danis T, Kaitetzidou E, Kasapidis P, Kristoffersen JB, Papadogiannis V, Pavloudi C et al. (2021) 0s and 1s in marine molecular research: a regional HPC perspective. Gigascience, 10 (8): giab053, doi: 10.1093/gigascience/giab053
  • Chatzinikolaou Ε, Damianidis P, Pavloudi C, Vasileiadou A, Faulwetter S, Keklikoglou K, Plaitis W, Mavraki D, Nikolopoulou S, Arvanitidis C. (2021) Benthic communities in three Mediterranean touristic ports: MAPMED project. Biodiversity Data Journal (LifeWatchGreece collection), 9: e66420, doi: 10.3897/BDJ.9.e66420

2020

  • Obst M, Exter K, Allcock AL, Arvanitidis CD, Bustamante M, Cancio I, Carreira-Flores D, Chatzinikolaou E, Chatzigeorgiou G, Chrismas N, Clark MS, Comtet T, Dailianis T, Davies N, Deneudt K, de Cerio OD, …., Pavloudi C (2020) A Marine Biodiversity Observation Network for genetic monitoring of hard-bottom communities (ARMS-MBON). Frontiers in Marine Science, 7: 572680, doi: 10.3389/fmars.2020.572680
  • Tsiola A, Michoud G, Fodelianakis S, Karakassis I, Kotoulas G, Pavlidou A, Pavloudi C, Pitta P, Simboura N, Daffonchio D, Tsapakis M (2020) Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone. Viruses, 12: 806, doi: 10.3390/v12080806
  • Zafeiropoulos H, Ha Quoc V, 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 rRNA, ITS and COI marker genes. Gigascience, 9 (3), doi: 10.1093/gigascience/giaa022
  • Gerovasileiou V, Pavloudi C, Sedano F (2020) First record of the nudibranch Anteaeolidiella lurana (Ev. Marcus & Er. Marcus, 1967) in Greek waters. p. 137-138. In: New Alien Mediterranean Biodiversity Records 2020, Bariche, M., Al-Mabruk, SAA, Ates MA, Büyük A, Crocetta F. et al., Mediterranean Marine Science, 21 (1), doi: 10.12681/mms.21987

2018

  • Vasileiadou K, Pavloudi C, Camisa F, Tsikopoulou I, Fragopoulou N, Kotoulas G, Arvanitidis C (2018) Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem. Journal of the Marine Biological Association of the United Kingdom, 98(4): 777-789, doi: 10.1017/S0025315416001910

2017

  • Pavloudi C, Kristoffersen JB, Oulas A, De Troch M, Arvanitidis C (2017) Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s ‘‘species minimum’’ concept. PeerJ,5:e3687. doi: 10.7717/peerj.3687 (corresponding author)
  • 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. Aquatic Microbial Ecology, 79: 209-219, doi: 10.3354/ame01829 (corresponding author)
  • Hummel H, van Avesaath P, Wijnhoven S, Kleine Schaars L, Degraer S, Kerckhof F, Bojanic N, Skejic S, Vidjak O, Rousou M, Orav-Kotta H, Kotta J, Jourde J, Pedrotti ML, Leclerc JC, Simon N, Rigaut-Jalabert F, Bachelet G, Lavesque N, Arvanitidis C, Pavloudi C, et al (2017) Geographic patterns of biodiversity in European coastal marine benthos. Journal of the Marine Biological Association of the United Kingdom (special issue on the 50th EMBS), 97(3): 507-523, doi: 10.1017/S0025315416001119
  • Puente A, Guinda X, Juanes J, Echavarri-Erasun B, Ramos E, Degraer S, Kerckhof F, Bojanic N, Rousou M, Orav-Kotta H, Kotta J, Jourde J, Pedrotti ML, Leclerc JC, Simon N, Bachelet G, Lavesque N, Arvanitidis C, Pavloudi C, et al (2017) The role of physical variables in biodiversity patterns of intertidal macroalgae along European coasts. Journal of the Marine Biological Association of the United Kingdom (special issue on the 50th EMBS), 97(3): 549-560, doi: 10.1017/S0025315416001673
  • Dal Bello M, Leclerc JC, Benedetti Cecchi L, Arvanitidis C, van Avesaath P, Bachelet G, Bojanic N, Como S, Coppa S, Coughlan J, Crowe T, Degraer S, Espinosa F, Faulwetter S, Frost M, Guinda X, Jankowska E, Jourde J, Kerckhof F, Kotta J, Lavesque N, De Lucia G, Magni P, de Matos V, Orav-Kotta H, Pavloudi C, et al (2017) Consistent patterns of spatial variability between NE Atlantic and Mediterranean rocky shores. Journal of the Marine Biological Association of the United Kingdom (special issue on the 50th EMBS), 97(3): 539-547, doi: 10.1017/S0025315416001491
  • Kotta J, Orav-Kotta H, Jänes H, Hummel H, Arvanitidis C, van Avesaath P, Bachelet G, Benedetti Cecchi L, Bojanic N, Como S, Coppa S, Coughlan J, Crowe T, Dal Bello M, Degraer S, Juanes J, de Matos V, Espinosa F, Faulwetter S, Frost M, Guinda X, Jankowska E, Jourde J, Kerckhof F, Lavesque N, Leclerc JC, Magni P, Pavloudi C, et al (2017) Essence of the patterns of cover and richness of intertidal hard bottom communities: a pan-European study. Journal of the Marine Biological Association of the United Kingdom (special issue on the 50th EMBS), 97(3): 525-538, doi: 10.1017/S0025315416001351

2016

  • Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJL, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C, Pafilis E (2016) Seqenv: linking sequences to environments through text mining. PeerJ, 4:e2690, doi: 10.7717/peerj.2690
  • Varsos C, Patkos T, Oulas A, Pavloudi C, Gougousis A, Ijaz UZ, Filiopoulou I, Pattakos N, Vanden Berghe E, Fernández-Guerra A, Faulwetter S, Chatzinikolaou E, Pafilis E, Arvanitidis C (2016) Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab). Biodiversity Data Journal (LifeWatchGreece collection), 4: e8357, doi: 10.3897/BDJ.4.e8357
  • Vasileiadou K, Pavloudi C, Sarropoulou E, Fragopoulou N, Kotoulas G, Arvanitidis C (2016) Unique COI haplotypes in Hediste diversicolor populations in lagoons adjoining the Ionian Sea. Aquatic Biology, 25: 7-15, doi: 10.3354/ab00654
  • Vasileiadou K, Pavloudi C, Kalantzi I, Apostolaki ET, Chatzigeorgiou G, Chatzinikolaou E, Pafilis E, Papageorgiou N, Fanini L, Konstas S, Fragopoulou N, Arvanitidis C (2016) Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece). Biodiversity Data Journal (LifeWatchGreece collection), 4: e8233, doi: 10.3897/BDJ.4.e8233
  • Pavloudi C, Christodoulou M, Mavidis M (2016) Macrofaunal assemblages associated with the sponge Sarcotragus foetidus Schmidt, 1862 (Porifera: Demospongiae) at the coasts of Cyprus and Greece. Biodiversity Data Journal (LifeWatchGreece collection), 4: e8210, doi: 10.3897/BDJ.4.e8210 (corresponding author)
  • 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, doi: 10.1016/j.margen.2016.01.005 (corresponding author)

2015

  • Hummel H, Frost M, Juanes JA, Ruci S, Cakmak T, Louizidou P, Andersen SF, Eriksson A, Bordeyne F, Vandenbosch F, Kochmann J, Pavloudi C, et al. (2015) A comparison on the degree of implementation of marine biodiversity indicators by European countries in relation to the Marine Strategy Framework Directive (MSFD). Journal of the Marine Biological Association of the United Kingdom (special issue on the 49th EMBS), 95(8): 1519-1531, doi: 10.1017/S0025315415000235
  • Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I. (2015) Metagenomics: tools and insights for analyzing next generation sequencing data derived from biodiversity studies. Bioinformatics and Biology Insights, 9: 75-88, doi: 10.4137/BBI.S12462
  • Pafilis E, Frankild SP, Schnetzer J, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, Leary P, Hammock J, Schulz K, Parr CS, Arvanitidis C, Jensen LJ. (2015) ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics, 31(11): 1872-1874. doi: 10.1093/bioinformatics/btv045
  • Faulwetter S, Papageorgiou N, Koulouri P, Fanini L, Chatzinikolaou E, Markantonatou V, Pavloudi C, Chatzigeorgiou G, Keklikoglou K, Vasileiadou K, Basset A, Pinna M, Rosati I, Reizopoulou S, Nicolaidou A, Arvanitidis C (2015). Resistance of polychaete species and trait patterns to simulated species loss in coastal lagoons. Journal of Sea Research (special issue on Protecting Marine Biodiversity to Preserve Ecosystem Functioning: a Tribute to Carlo Heip), 98: 73-82, doi: 10.1016/j.seares.2014.09.003

2014

  • Faulwetter S, Markantonatou V, Pavloudi C, Papageorgiou N, Keklikoglou K, Chatzinikolaou E, Pafilis E, Chatzigeorgiou G, Vasileiadou K, Dailianis T, Fanini L, Koulouri P, Arvanitidis C (2014). Polytraits: A database on biological traits of marine polychaetes. Biodiversity Data Journal, 2: e1024. doi: 10.3897/BDJ.2.e1024

2013

  • Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou K, Arvanitidis C, Jensen LJ (2013). The SPECIES and ORGANISMS resources for fast and accurate identification of taxonomic names in text. PLOS One (Text Mining Collection), 8(6): e65390. doi: 10.1371/journal.pone.0065390

2011

  • Arvanitidis C, Faulwetter S, Chatzigeorgiou G, Penev L, Bankí O, Dailianis T, Pafilis E, Kouratoras M, Chatzinikolaou E, Fanini L, Vasileiadou A, Pavloudi C, Vavilis P, Koulouri P, Dounas C (2011). Engaging the broader community in biodiversity research: the concept of the COMBER pilot project for divers in ViBRANT. Zookeys, 150: 211-229. doi: 10.3897/zookeys.150.2149

Book chapters:

2022

  • Pavloudi C, Chatzinikolaou Ε, Keklikoglou Κ, Vasileiadou Κ, Arvanitidis C (2022) Seascape of soft bottom benthic communities in the Aegean Sea. In: The Handbook of Environmental Chemistry. Springer, Berlin, Heidelberg. doi: 10.1007/698_2021_839 (corresponding author)

Handbooks/Reports:

2022

  • Santi I, Cancio I, Corre E, Cox CJ, Exter K, Hoebeke M, Kervella AE, Laroquette A, Pavloudi C, Portier M, Pade N (2022) European Marine Omics Biodiversity Observation Network (EMO BON) – Data Management Plan. (Version 1.0). Paris, France, EMBRC-ERIC, 33pp. doi: 10.25607/OBP-1743

2021

  • Santi I, Casotti R, Comtet T, Cunliffe M, Koulouri Y, Macheriotou L, Not F, Obst M, Pavloudi C, Romac S, Thiebaut E, Vanaverbeke J, Pade N (2021) European Marine Omics Biodiversity Observation Network (EMO BON) Handbook. (Version 1.0). Paris, France, EMBRC-ERIC, 63pp. doi: 10.25607/OBP-1653

2015

  • Lahajnar N, Mohrholz V, Angenendt S, Ankele M, Annighöfer M, Beier S, Birkicht M, Bohata K, Brust-Möbius J, Buchholz F, Chikwililwa C, Cordts HM, Dähnke K, …, Pavloudi C, et al (2015) Geochemistry and Ecology of the Namibian Upwelling System NAMUFIL: Namibian Upwelling Filament Study - Cruise No. M103 - December 27, 2013 – February 11, 2014 – Walvis Bay (Namibia) - Walvis Bay (Namibia). METEOR-Berichte, M103, 91 pp., DFG-Senatskommission für Ozeanographie, doi: 10.2312/cr_m103

Theses:

2017

PhD thesis: Microbial community functioning at hypoxic sediments revealed by targeted metagenomics and RNA stable isotope probing

Examination committee: Prof. Dr. Marleen De Troch (Promotor), Prof. Dr. Michael W. Friedrich (Promotor), Dr. Christos Arvanitidis (Promotor), Dr. ir. Jo De Vrieze, Prof. Dr. Anne Willems, Prof. Dr. Dominique Adriaens, Dr. Ulrike Braeckman, PD Dr. Holger Auel, Prof Dr. Jens Harder

2012

MSc thesis: Comparative analysis of geochemical variables, macrofaunal and microbial communities in lagoonal ecosystems

Examination committee: Prof. Ioannis Karakassis, Dr. Christos Arvanitidis (Promotor), Dr. Georgios Kotoulas

2009

BSc thesis: Comparative study of the organismic assemblages associated with the demosponge Sarcotragus foetidus Schmidt, 1862 in the coasts of Cyprus and Greece

Supervisor: Prof. Αthanasios Koukouras