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2026
Gioti, Anastasia; Kristoffersen, Jon Bent; Kaşlı, Bekir; Tarifa, Georgia; Rizzo, Carmen; Dailianis, Thanos
In: Biodiversity Data Journal, vol. 14, pp. e187301, 2026, ISSN: 1314-2828, 1314-2836.
@article{gioti_microbial_2026,
title = {Microbial communities associated with two populations of the sponge \textit{Chondrilla nucula} under present and projected climate conditions in the Aegean Sea},
author = {Anastasia Gioti and Jon Bent Kristoffersen and Bekir Kaşlı and Georgia Tarifa and Carmen Rizzo and Thanos Dailianis},
url = {https://bdj.pensoft.net/article/187301/
/wp-content/uploads/2026/05/2026-Gioti-BDJ-19.pdf},
doi = {10.3897/BDJ.14.e187301},
issn = {1314-2828, 1314-2836},
year = {2026},
date = {2026-05-08},
urldate = {2026-05-08},
journal = {Biodiversity Data Journal},
volume = {14},
pages = {e187301},
abstract = {This data paper describes bacterial and fungal communities associated with the sponge
Chondrilla nucula
collected from two Eastern Mediterranean populations (North and South Aegean Sea) and maintained under controlled common-garden conditions simulating present and projected climate scenarios over a period of 3 months. Microbial composition was characterised using two complementary ribosomal marker approaches: Illumina (MiSeq) sequencing of the 16S rRNA gene for Bacteria and Oxford Nanopore (MinION) sequencing of a long 18S-ITS-28S rRNA fragment for Fungi. A total of 24 sponge libraries (3 climate conditions x 2 populations x 4 biological replicates) along with six control libraries (water from three experimental tanks, extraction and PCR blanks) were constructed for each group of microsymbionts. The resulting reads were processed using custom and publicly available bioinformatic pipelines and databases, followed by initial taxonomic assignment. This dataset represents the first fungal community associated with
C. nucula
and the first bacterial community for this species from the Aegean Sea.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This data paper describes bacterial and fungal communities associated with the sponge
Chondrilla nucula
collected from two Eastern Mediterranean populations (North and South Aegean Sea) and maintained under controlled common-garden conditions simulating present and projected climate scenarios over a period of 3 months. Microbial composition was characterised using two complementary ribosomal marker approaches: Illumina (MiSeq) sequencing of the 16S rRNA gene for Bacteria and Oxford Nanopore (MinION) sequencing of a long 18S-ITS-28S rRNA fragment for Fungi. A total of 24 sponge libraries (3 climate conditions x 2 populations x 4 biological replicates) along with six control libraries (water from three experimental tanks, extraction and PCR blanks) were constructed for each group of microsymbionts. The resulting reads were processed using custom and publicly available bioinformatic pipelines and databases, followed by initial taxonomic assignment. This dataset represents the first fungal community associated with
C. nucula
and the first bacterial community for this species from the Aegean Sea.
Chondrilla nucula
collected from two Eastern Mediterranean populations (North and South Aegean Sea) and maintained under controlled common-garden conditions simulating present and projected climate scenarios over a period of 3 months. Microbial composition was characterised using two complementary ribosomal marker approaches: Illumina (MiSeq) sequencing of the 16S rRNA gene for Bacteria and Oxford Nanopore (MinION) sequencing of a long 18S-ITS-28S rRNA fragment for Fungi. A total of 24 sponge libraries (3 climate conditions x 2 populations x 4 biological replicates) along with six control libraries (water from three experimental tanks, extraction and PCR blanks) were constructed for each group of microsymbionts. The resulting reads were processed using custom and publicly available bioinformatic pipelines and databases, followed by initial taxonomic assignment. This dataset represents the first fungal community associated with
C. nucula
and the first bacterial community for this species from the Aegean Sea.
2025
Siaperas, Romanos; Taxeidis, George; Gioti, Anastasia; Nikolaivits, Efstratios; Topakas, Evangelos
Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification Journal Article
In: Environmental Pollution, vol. 376, pp. 126386, 2025, ISSN: 02697491.
@article{siaperas_multi-omics_2025,
title = {Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification},
author = {Romanos Siaperas and George Taxeidis and Anastasia Gioti and Efstratios Nikolaivits and Evangelos Topakas},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0269749125007596
/wp-content/uploads/2025/05/2025-Siaperas-EnvPol-24.pdf},
doi = {10.1016/j.envpol.2025.126386},
issn = {02697491},
year = {2025},
date = {2025-05-22},
urldate = {2025-05-22},
journal = {Environmental Pollution},
volume = {376},
pages = {126386},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2024
Gioti, Anastasia; Theodosopoulou, Danai; Bravakos, Panos; Magoulas, Antonios; Kotoulas, Georgios
The bioinformatics landscape in environmental omics: Lessons from a national ELIXIR survey Journal Article
In: iScience, vol. 27, no. 6, pp. 110062, 2024, ISSN: 25890042.
@article{gioti_bioinformatics_2024,
title = {The bioinformatics landscape in environmental omics: Lessons from a national ELIXIR survey},
author = {Anastasia Gioti and Danai Theodosopoulou and Panos Bravakos and Antonios Magoulas and Georgios Kotoulas},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/06/2024-Gioti-iScience-26.pdf
https://linkinghub.elsevier.com/retrieve/pii/S2589004224012872},
doi = {10.1016/j.isci.2024.110062},
issn = {25890042},
year = {2024},
date = {2024-06-08},
urldate = {2024-06-10},
journal = {iScience},
volume = {27},
number = {6},
pages = {110062},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2021
Nikolaivits, Efstratios; Siaperas, Romanos; Agrafiotis, Andreas; Ouazzani, Jamal; Magoulas, Antonios; Gioti, Αnastasia; Topakas, Evangelos
In: Science of The Total Environment, vol. 775, pp. 145818, 2021, ISSN: 00489697.
@article{nikolaivits_functional_2021,
title = {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},
author = {Efstratios Nikolaivits and Romanos Siaperas and Andreas Agrafiotis and Jamal Ouazzani and Antonios Magoulas and Αnastasia Gioti and Evangelos Topakas},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969721008858},
doi = {10.1016/j.scitotenv.2021.145818},
issn = {00489697},
year = {2021},
date = {2021-06-01},
urldate = {2021-03-17},
journal = {Science of The Total Environment},
volume = {775},
pages = {145818},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zafeiropoulos, Haris; Gioti, Anastasia; Ninidakis, Stelios; Potirakis, Antonis; Paragkamian, Savvas; Angelova, Nelina; Antoniou, Aglaia; Danis, Theodoros; Kaitetzidou, Eliza; Kasapidis, Panagiotis; Kristoffersen, Jon Bent; Papadogiannis, Vasileios; Pavloudi, Christina; Ha, Quoc Viet; Lagnel, Jacques; Pattakos, Nikos; Perantinos, Giorgos; Sidirokastritis, Dimitris; Vavilis, Panagiotis; Kotoulas, Georgios; Manousaki, Tereza; Sarropoulou, Elena; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Pafilis, Evangelos
0s and 1s in marine molecular research: a regional HPC perspective Journal Article
In: GigaScience, vol. 10, no. 8, pp. giab053, 2021, ISSN: 2047-217X.
@article{zafeiropoulos_0s_2021,
title = {0s and 1s in marine molecular research: a regional HPC perspective},
author = {Haris Zafeiropoulos and Anastasia Gioti and Stelios Ninidakis and Antonis Potirakis and Savvas Paragkamian and Nelina Angelova and Aglaia Antoniou and Theodoros Danis and Eliza Kaitetzidou and Panagiotis Kasapidis and Jon Bent Kristoffersen and Vasileios Papadogiannis and Christina Pavloudi and Quoc Viet Ha and Jacques Lagnel and Nikos Pattakos and Giorgos Perantinos and Dimitris Sidirokastritis and Panagiotis Vavilis and Georgios Kotoulas and Tereza Manousaki and Elena Sarropoulou and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Evangelos Pafilis},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Zafeiropoulos-GiGa-63.pdf
https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab053/6353916},
doi = {10.1093/gigascience/giab053},
issn = {2047-217X},
year = {2021},
date = {2021-01-01},
urldate = {2021-08-23},
journal = {GigaScience},
volume = {10},
number = {8},
pages = {giab053},
abstract = {Abstract
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
2020
Gioti, Anastasia; Siaperas, Romanos; Nikolaivits, Efstratios; Goff, Géraldine Le; Ouazzani, Jamal; Kotoulas, Georgios; Topakas, Evangelos
Draft Genome Sequence of a Cladosporium Species Isolated from the Mesophotic Ascidian Didemnum maculosum Journal Article
In: Microbiology Resource Announcements, vol. 9, no. 18, 2020, (Publisher: American Society for Microbiology Journals _eprint: https://mra.asm.org/content/9/18/e00311-20.full.pdf).
@article{gioti_draft_2020,
title = {Draft Genome Sequence of a Cladosporium Species Isolated from the Mesophotic Ascidian Didemnum maculosum},
author = {Anastasia Gioti and Romanos Siaperas and Efstratios Nikolaivits and Géraldine Le Goff and Jamal Ouazzani and Georgios Kotoulas and Evangelos Topakas},
editor = {Antonis Rokas},
url = {https://mra.asm.org/content/9/18/e00311-20},
doi = {10.1128/MRA.00311-20},
year = {2020},
date = {2020-01-01},
journal = {Microbiology Resource Announcements},
volume = {9},
number = {18},
abstract = {We report the 28-Mbp draft genome sequence of the marine fungus Cladosporium sp. strain TM138. The species was isolated from the marine invertebrate Didemnum maculosum. Its genome sequence will inform future investigations into the species’ enzymatic potential for bioremediation and its evolution in marine environments.},
note = {Publisher: American Society for Microbiology Journals
_eprint: https://mra.asm.org/content/9/18/e00311-20.full.pdf},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We report the 28-Mbp draft genome sequence of the marine fungus Cladosporium sp. strain TM138. The species was isolated from the marine invertebrate Didemnum maculosum. Its genome sequence will inform future investigations into the species’ enzymatic potential for bioremediation and its evolution in marine environments.