| PEMA: a flexible pipeline for environmental DNA metabarcoding analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes H Zafeiropoulos, HQ Viet, K Vasileiadou, A Potirakis, C Arvanitidis, ... GigaScience 9 (3), giaa022, 2020 | 53* | 2020 |
| 0s and 1s in marine molecular research: a regional HPC perspective H Zafeiropoulos, A Gioti, S Ninidakis, A Potirakis, S Paragkamian, ... GigaScience 10 (8), giab053, 2021 | 21 | 2021 |
| Geometric algorithms for sampling the flux space of metabolic networks A Chalkis, V Fisikopoulos, E Tsigaridas, H Zafeiropoulos arXiv preprint arXiv:2012.05503, 2020 | 14 | 2020 |
| PREGO: a literature and data-mining resource to associate microorganisms, biological processes, and environment types H Zafeiropoulos, S Paragkamian, S Ninidakis, GA Pavlopoulos, ... Microorganisms 10 (2), 293, 2022 | 13 | 2022 |
| A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses A Hakimzadeh, A Abdala Asbun, D Albanese, M Bernard, D Buchner, ... Molecular Ecology Resources, 2023 | 11 | 2023 |
| The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data H Zafeiropoulos, L Gargan, S Hintikka, C Pavloudi, J Carlsson MBMG Metabarcoding and Metagenomics, 3968, 2021 | 11 | 2021 |
| PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. GigaScience. 2020; 9: giaa022 H Zafeiropoulos, HQ Viet, K Vasileiadou, A Potirakis, C Arvanitidis, ... | 5 | |
| Metabolic models of human gut microbiota: Advances and challenges DR Garza, D Gonze, H Zafeiropoulos, B Liu, K Faust Cell systems 14 (2), 109-121, 2023 | 4 | 2023 |
| The Santorini Volcanic Complex as a Valuable Source of Enzymes for Bioenergy PN Polymenakou, P Nomikou, H Zafeiropoulos, M Mandalakis, ... Energies 14 (5), 1414, 2021 | 3 | 2021 |
| The IMBBC HPC facility: history, configuration, usage statistics and related activities H Zafeiropoulos, A Gioti, S Ninidakis, P Antonis, S Paragkamian, A Nelina, ... | 3* | |
| Predicting microbial interactions with approaches based on flux balance analysis: an evaluation C Joseph, H Zafeiropoulos, K Bernaerts, K Faust BMC bioinformatics 25 (1), 36, 2024 | 2 | 2024 |
| Improving genome-scale metabolic models of incomplete genomes with deep learning MD Boer, C Melkonian, H Zafeiropoulos, AF Haas, D Garza, BE Dutilh bioRxiv, 2023.07. 10.548314, 2023 | 1 | 2023 |
| metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data H Zafeiropoulos, M Beracochea, S Ninidakis, K Exter, A Potirakis, ... GigaScience 12, giad078, 2023 | 1 | 2023 |
| Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community C Pavloudi, H Zafeiropoulos FEMS Microbiology Ecology 98 (12), fiac141, 2022 | 1 | 2022 |
| Bacteria are everywhere, even in your COI marker gene data! H Zafeiropoulos, L Gargan, S Hintikka, C Pavloudi, J Carlsson bioRxiv, 2021.07. 10.451903, 2021 | 1 | 2021 |
| PEMA: from the raw. fastq files of 16S rRNA and COI marker genes to the (M) OTU-table, a thorough metabarcoding analysis H Zafeiropoulos, HQ Viet, K Vasileiadou, A Potirakis, C Arvanitidis, ... bioRxiv, 709113, 2019 | 1 | 2019 |
| Establishing the ELIXIR Microbiome Community RD Finn, B Balech, J Burgin, P Chua, E Corre, CJ Cox, C Donati, ... F1000Research 13, ELIXIR-50, 2024 | | 2024 |
| dingo: a Python package for metabolic flux sampling A Chalkis, V Fisikopoulos, E Tsigaridas, H Zafeiropoulos | | 2024 |
| EOSC-Life Report on the work of the Open Call Projects A Rybina, P Audergon, C Pfander, B Batut, M Beracochea, J Bischof, ... EMBL-HD; CSIC, 2023 | | 2023 |
| Automating the curation process of historical literature on marine biodiversity using text mining: The DECO Workflow S Paragkamian, G Sarafidou, D Mavraki, C Pavloudi, J Beja, M Eliezer, ... Frontiers in Marine Science 9, 940844, 2022 | | 2022 |
