Mark Hoebeke
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View article: FUTURE-OBS : Developing a new generation of augmented observatories to ensure sustainable and equitable management of coastal socio-ecosystems
FUTURE-OBS : Developing a new generation of augmented observatories to ensure sustainable and equitable management of coastal socio-ecosystems Open
The livelihoods of more than 3 billion people depend on marine coastal socio-ecosystems. Yet, local anthropogenic stressors and global human-driven climate change increasingly threaten the sustainability and resilience of the tightly inter…
View article: Marine Biodiversity Data FAIRification
Marine Biodiversity Data FAIRification Open
Step-by-step walkthrough of the FAIRification process applied to marine biodiversity data.
View article: Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies
Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies Open
The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine p…
View article: ASTAN temperature & salinity historical time series (1952 - 1999)
ASTAN temperature & salinity historical time series (1952 - 1999) Open
The Astan-Roscoff time-series data characterize the temperature and salinity of the Western English Channel. Between 1952 and 1982 the sampling station was located to the north-west of Batz Island. Since 1983, the sampling station is locat…
View article: Global Phylogeography of Marine <i>Synechococcus</i> in Coastal Areas Reveals Strong Community Shifts
Global Phylogeography of Marine <i>Synechococcus</i> in Coastal Areas Reveals Strong Community Shifts Open
Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent …
View article: Station Biologique de Roscoff - Training - Linux Initiation - Training materials + Toy dataset
Station Biologique de Roscoff - Training - Linux Initiation - Training materials + Toy dataset Open
Context Training materials and Toy dataset used during the Linux Initiation ABiMS training session at the Station Biologique de Roscoff.
View article: SulfAtlas, the sulfatase database: state of the art and new developments
SulfAtlas, the sulfatase database: state of the art and new developments Open
SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1–S4) and the largest family (S1, formylglycine-dependent sulf…
View article: Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies
Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies Open
The ever-increasing number of available microbial genomes and metagenomes provide new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, notably for the abundant and ubiquitous marine picoc…
View article: Seasonal dynamics of marine protist communities in tidally mixed coastal waters
Seasonal dynamics of marine protist communities in tidally mixed coastal waters Open
Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes of plankton community turnover rates have not been fully elucidated so far. Here, we analyse patterns of p…
View article: Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas
Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas Open
Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, w…
View article: Comparative thermophysiology of marine <i>Synechococcus</i> CRD1 strains isolated from different thermal niches in iron-depleted areas
Comparative thermophysiology of marine <i>Synechococcus</i> CRD1 strains isolated from different thermal niches in iron-depleted areas Open
Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, w…
View article: Global phylogeography of marine <i>Synechococcus</i> in coastal areas reveals strikingly different communities than in the open ocean
Global phylogeography of marine <i>Synechococcus</i> in coastal areas reveals strikingly different communities than in the open ocean Open
Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in…
View article: Seasonal temporal dynamics of marine protists communities in tidally mixed coastal waters
Seasonal temporal dynamics of marine protists communities in tidally mixed coastal waters Open
Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes determining marine species and community turnover rates have not been fully elucidated so far. Here, we an…
View article: Morphological phytoplankton counts for the SOMLIT-Astan time-series (2007-2017)
Morphological phytoplankton counts for the SOMLIT-Astan time-series (2007-2017) Open
The present text file includes morphologic microscopic counts for SOMLIT-Astan station (Western English Channel). Samples (250 mL) of natural seawater intended for the acquisition of microscopic counts were preserved with acid Lugol’s iodi…
View article: Morphological phytoplankton counts for the SOMLIT-Astan time-series (2007-2017)
Morphological phytoplankton counts for the SOMLIT-Astan time-series (2007-2017) Open
The present text file includes morphologic microscopic counts for SOMLIT-Astan station (Western English Channel). Samples (250 mL) of natural seawater intended for the acquisition of microscopic counts were preserved with acid Lugol’s iodi…
View article: Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes
Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes Open
Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Ear…
View article: Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria
Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria Open
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specifi…
View article: Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803
Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803 Open
Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically charac…
View article: METdb: A GENOMIC REFERENCE DATABASE FOR MARINE SPECIES
METdb: A GENOMIC REFERENCE DATABASE FOR MARINE SPECIES Open
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View article: PHYTOBS dataset - French National Service of Observation for Phytoplankton in coastal waters
PHYTOBS dataset - French National Service of Observation for Phytoplankton in coastal waters Open
The PHYTOBS dataset includes long-term time series on marine microphytoplankton, since 1987, along the whole French metropolitan coast. Microphytoplankton data cover microscopic taxonomic identifications and counts. The whole dataset is av…
View article: Fast Tree Inference With Weighted Fusion Penalties
Fast Tree Inference With Weighted Fusion Penalties Open
Given a dataset with many features observed in a large number of conditions, it is desirable to fuse and aggregate conditions that are similar to ease the interpretation and extract the main characteristics of the data. This article presen…
View article: Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity
Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity Open
Sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. However, the number of sulfatases whose substrate has been characterized is limited in comparison to the hug…