Gherman Uritskiy
Johns Hopkins University
Shotgun sequencingEcosystemData miningClimate changeGenomeMicrobiomeMetagenomicsTransfer RNANicheAdaptationRegulation of gene expressionThree-domain systemEcologyIntergenic regionExtremophileDisturbance (ecology)EukaryotePathogen detectionEnvironmental scienceComputer sciencePipeline (software)RNAComputational biologyEvolutionary biologyHalophileMicrobial population biologyBiologyPhylum
21Publications
6H-index
314Citations
Publications 16
Newest
#1Swati Jain (CUA: The Catholic University of America)H-Index: 3
#2Gherman UritskiyH-Index: 6
Last. Kijak G
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A productive HIV-1 infection is often established by a single transmitted/founder (T/F) virus, which then evolves into a complex mixture of variants during the lifetime of infection. An effective vaccine should have sufficient breadth to block the entry of diverse T/F involved in different infections. Although the variable V1V2 domain of HIV-1 envelope protein (Env) is found to be a good target for vaccine design based on the correlates of protection in the modestly successful RV144 trial, the b...
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#1Gherman UritskiyH-Index: 6
#1Uritskiy GH-Index: 1
Last. Shawn SullivanH-Index: 11
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Viruses play crucial roles in the ecology of microbial communities, yet they remain relatively understudied in their native environments. Despite many advancements in high-throughput whole-genome sequencing (WGS), sequence assembly, and annotation of viruses, the reconstruction of full-length viral genomes directly from metagenomic sequencing is possible only for the most abundant phages and requires long-read sequencing technologies. Additionally, the prediction of their cellular hosts remains ...
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#1Derek M. Bickhart (ARS: Agricultural Research Service)H-Index: 32
#2Kolmogorov M (UC: University of California)H-Index: 1
Last. Timothy P. L. Smith (ARS: Agricultural Research Service)H-Index: 64
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Microbial communities in many environments include distinct lineages of closely related organisms which have proved challenging to separate in metagenomic assembly, preventing generation of complete metagenome-assembled genomes (MAGs). The advent of long and accurate HiFi reads presents a possible means to address this challenge by generating complete MAGs for nearly all sufficiently abundant bacterial genomes in a microbial community. We present a metagenomic HiFi assembly of a complex microbia...
1 CitationsSource
#1Gherman UritskiyH-Index: 6
#2Adam MunnH-Index: 3
Last. Jocelyne DiRuggieroH-Index: 31
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Spatial heterogeneity in microbial communities is observed in all natural ecosystems and can stem from both adaptations to local environmental conditions as well as stochastic processes. Extremophile microbial communities inhabiting evaporitic halite nodules (salt rocks) in the Atacama Desert, Chile, are a good model ecosystem for investigating factors leading to microbiome heterogeneity, due to their diverse taxonomic composition and the spatial segregation of individual nodules. We investigate...
1 CitationsSource
#1Gherman Uritskiy (Johns Hopkins University)H-Index: 6
#2Michael J. Tisza (Johns Hopkins University)H-Index: 7
Last. Jocelyne DiRuggiero (Johns Hopkins University)H-Index: 31
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Microbial communities play essential roles in the biosphere and understanding the mechanisms underlying their functional adaptations to environmental conditions is critical for predicting their behavior. This aspect of microbiome function has not been well characterized in natural high-salt environments. To address this knowledge gap, and to build a general framework relating the genomic and transcriptomic components in a microbiome, we performed a meta-omic survey of extremophile communities in...
4 CitationsSource
#1Diego R. Gelsinger (Johns Hopkins University)H-Index: 7
#2Gherman Uritskiy (Johns Hopkins University)H-Index: 6
Last. Jocelyne DiRuggiero (Johns Hopkins University)H-Index: 31
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ABSTRACT Regulatory small RNAs (sRNAs) play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been extensively studied in model organisms, but very little is known about the dynamics of sRNA synthesis and their roles in the natural environment. In this study, we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed in an extremophilic microbial community inhabiting halite nodules (salt rocks) in the Atacama De...
3 CitationsSource
#1Eric G. Sakowski (Johns Hopkins University)H-Index: 4
#1Eric G. Sakowski (Johns Hopkins University)H-Index: 4
Last. Sarah P. Preheim (Johns Hopkins University)H-Index: 19
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ABSTRACT Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic...
2 CitationsSource
#1Diego R. Gelsinger (Johns Hopkins University)H-Index: 7
#2Gherman Uritskiy (Johns Hopkins University)H-Index: 6
Last. Jocelyne DiRuggiero (Johns Hopkins University)H-Index: 31
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Regulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks...
1 CitationsSource
#1Gherman Uritskiy (Johns Hopkins University)H-Index: 6
#2Samantha Getsin (Johns Hopkins University)H-Index: 1
Last. Jocelyne DiRuggiero (Johns Hopkins University)H-Index: 31
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Understanding the mechanisms underlying microbial resistance and resilience to perturbations is essential to predict the impact of climate change on Earth’s ecosystems. However, the resilience and adaptation mechanisms of microbial communities to natural perturbations remain relatively unexplored, particularly in extreme environments. The response of an extremophile community inhabiting halite (salt rocks) in the Atacama Desert to a catastrophic rainfall provided the opportunity to characterize ...
23 CitationsSource