Dean Vik
YOU?
Author Swipe
View article: Mobile genetic elements that shape microbial diversity and functions in thawing permafrost soils
Mobile genetic elements that shape microbial diversity and functions in thawing permafrost soils Open
The world's ecosystems are shaped by microbiota. Their niches and their impacts depend on functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate …
Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome Open
Background: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, effort…
View article: Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient
Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient Open
Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 me…
MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets Open
Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal vir…
View article: Ocean-wide comparisons of mesopelagic planktonic community structures
Ocean-wide comparisons of mesopelagic planktonic community structures Open
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 vast and heterogeneous part of t…
Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines Open
Background Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero…
Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines Open
Background: Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea-ice brine, similar in subzer…
Additional file 1 of Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines Open
Additional file 1: Table S1. Viromic statistics and viral concentrations of four samples. Table S2. Comparison in virus recovery from short- and long-read assemblies. Table S3. Size summary of vOTUs from CB17. The two assembly types (i.e.,…
Data and model for - MArVD2: A machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. Open
Here we are depositing all databases needed to run MArVD2 for archaeal virus identification, datasets used in the creation of the model, two test datasets, and the model itself. These data are used in the article: "MArVD2: A machine learni…
Databases for - MArVD2: A machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. Open
Here we are depositing all databases needed to run MArVD2 for archaeal virus identification. We are also including all datasets used for training and benchmarking MArVD2. These data are used in the article: "MArVD2: A machine learning enha…
Ecogenomics reveals viral communities across the Challenger Deep oceanic trench Open
Despite the environmental challenges and nutrient scarcity, the geographically isolated Challenger Deep in Mariana trench, is considered a dynamic hotspot of microbial activity. Hadal viruses are the least explored microorganisms in Challe…
High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome Open
Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus ident…
Viral sequence identification SOP with VirSorter2 v3 Open
This protocol shows how to use VirSorter2, checkV, DRAMv and some manual curation criteria for viral sequence identification.
Peer Review #2 of "Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation (v0.2)" Open
Background:Viruses influence global patterns of microbial diversity and nutrient cycles.Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its …
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation Open
Background Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its…
View article: Ocean-wide comparisons of mesopelagic planktonic community structures
Ocean-wide comparisons of mesopelagic planktonic community structures Open
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 vast and heterogeneous part of t…
Additional file 4 of VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses Open
Additional file 3. First 20 rows of the “final-viral-score.tsv” VirSorter2 output file for Tara Oceans virome 85_SRF. VirSorter 2.0.beta was used with default parameters, including all classifiers and a minimum score cutoff of 0.5. The col…
Additional file 5 of VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses Open
Additional file 4. Manual inspection of contigs newly identified by VirSorter2 in Tara Oceans virome 85_SRF. The spreadsheet includes four tabs, including the list and characteristics of contigs ≥ 5kb selected for manual inspection (“Conti…
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters Open
Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved…
Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline Open
Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxili…
Genome-resolved viral ecology in a marine oxygen minimum zone (OMZ) Open
Summary Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here we assess the viral community eco…
View article: DRAM for distilling microbial metabolism to automate the curation of microbiome function
DRAM for distilling microbial metabolism to automate the curation of microbiome function Open
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation softwar…
View article: DRAM for distilling microbial metabolism to automate the curation of microbiome function
DRAM for distilling microbial metabolism to automate the curation of microbiome function Open
Microbial and viral communities transform the chemistry of Earth’s ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation softwar…
Viral ppulations from the Cariaco Basin Open
Here we present the 647 viral populations (clustered at 95% ID over 80% of the sequence) larger than 5kb from the Cariaco Basin and an additional 101 viral populations from the Tara Oceans GOV2.0 dataset which were also identified in Caria…
Viral ppulations from the Cariaco Basin Open
Here we present the 647 viral populations (clustered at 95% ID over 80% of the sequence) larger than 5kb from the Cariaco Basin and an additional 101 viral populations from the Tara Oceans GOV2.0 dataset which were also identified in Caria…