Paramvir Dehal
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View article: RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species Open
We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom ex…
View article: RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species Open
Leveraging the use of multiplex multi-omic networks, key insights into genetic and epigenetic mechanisms supporting biofuel production have been uncovered. Here, we introduce RWRtoolkit, a multiplex generation, exploration, and statistical…
View article: RWRtoolkit Narrative
RWRtoolkit Narrative Open
This narrative presents a demonstration of RWRtools methods to the important bioenergy feedstock Panicum virgatum (Switchgrass) by leveraging networks from the model plant Arabidopsis thaliana. We used a genome-wide association study (GWAS…
View article: A bacterial sensor taxonomy across earth ecosystems for machine learning applications
A bacterial sensor taxonomy across earth ecosystems for machine learning applications Open
Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transd…
View article: Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase
Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase Open
In the version of this article initially published, the affiliation for Qizhi Zhang and Chris S. Henry was incorrectly shown as the University of Tennessee instead of Argonne National Laboratory. The affiliations have been corrected in the…
View article: Author Correction: A genomic catalog of Earth’s microbiomes
Author Correction: A genomic catalog of Earth’s microbiomes Open
A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.
View article: Genome Extraction from Shotgun Metagenome Sequence Data
Genome Extraction from Shotgun Metagenome Sequence Data Open
Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Eart…
View article: Moab Desert Crust - Sample 4E
Moab Desert Crust - Sample 4E Open
Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Eart…
View article: A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative
A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative Open
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to ove…
View article: The DOE Systems Biology Knowledgebase (KBase)
The DOE Systems Biology Knowledgebase (KBase) Open
The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology — predicting and designing biological function from the biomolecular (…
View article: High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater
High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater Open
Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge…