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Article
Open AccessDatascape: exploring heterogeneous dataspace
Data science is a powerful field for gaining insights, comparing, and predicting behaviors from datasets. However, the diversity of methods and hypotheses needed to abstract a dataset exhibits a lack of generi...
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Article
Open AccessDisentangling microbial networks across pelagic zones in the tropical and subtropical global ocean
Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological...
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Article
Open AccessOcean-wide comparisons of mesopelagic planktonic community structures
For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a va...
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Article
Open AccessDisentangling temporal associations in marine microbial networks
Microbial interactions are fundamental for Earth’s ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in ...
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Article
Open AccessMicrobial community functioning during plant litter decomposition
Microbial life in soil is fueled by dissolved organic matter (DOM) that leaches from the litter layer. It is well known that decomposer communities adapt to the available litter source, but it remains unclear ...
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Article
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean
The role of the Arctic Ocean ecosystem in climate regulation may depend on the responses of marine microorganisms to environmental change. We applied genome-resolved metagenomics to 41 Arctic seawater samples,...
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Article
Open AccessDecline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula
Since the middle of the past century, the Western Antarctic Peninsula has warmed rapidly with a significant loss of sea ice but the impacts on plankton biodiversity and carbon cycling remain an open question. ...
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Article
Open AccessInvestigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic
Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the dive...
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Article
Open AccessAuthor Correction: Roadmap for naming uncultivated Archaea and Bacteria
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
Tara Oceans: towards global ocean ecosystems biology
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the comp...
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Article
Open AccessRoadmap for naming uncultivated Archaea and Bacteria
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need t...
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Article
Open AccessProbabilistic modeling to estimate jellyfish ecophysiological properties and size distributions
While Ocean modeling has made significant advances over the last decade, its complex biological component is still oversimplified. In particular, modeling organisms in the ocean system must integrate parameter...
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Article
Open AccessStructure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks ...
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Article
Plankton networks driving carbon export in the oligotrophic ocean
The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of th...
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Article
Open AccessDeciphering transcriptional regulations coordinating the response to environmental changes
Gene co-expression evidenced as a response to environmental changes has shown that transcriptional activity is coordinated, which pinpoints the role of transcriptional regulatory networks (TRNs). Nevertheless,...
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Chapter and Conference Paper
OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques
Constraint Based Methods had been successfully used to simulate genome-scale metabolic behaviors over a range of experimental conditions. In most applications, environmental constraints are parameterized, and ...
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Chapter and Conference Paper
Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming
Metabolic network reconstruction is of great biological relevance because it offers a way to investigate the metabolic behavior of organisms. However, reconstruction remains a difficult task at both the biolog...
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Chapter and Conference Paper
An ASP Application in Integrative Biology: Identification of Functional Gene Units
Integrating heterogeneous knowledge is necessary to elucidate the regulations in biological systems. In particular, such an integration is widely used to identify functional units, that are sets of genes that ...
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Article
Open AccessHybrid modeling of biological networks: mixing temporal and qualitative biological properties
Modeling a dynamical biological system is often a difficult task since the a priori unknown parameters of such models are not always directly given by the experiments. Despite the lack of experimental quantitativ...
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Chapter and Conference Paper
Including Ordinary Differential Equations Based Constraints in the Standard CP Framework
Coupling constraints and ordinary differential equations has numerous applications. This paper shows how to introduce constraints involving ordinary differential equations into the numerical constraint satisfa...
