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    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
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    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    Tips for a Winning Community Science Program Proposal
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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Home › Items tagged with: microbial genomics

Content Tagged "microbial genomics"

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October 11, 2023

Doubling Down on Known Protein Families

An illustration of a microscope emitting a beam of light that hits a small, nondescript item.Through a novel approach detailed in Nature, a massive computational analysis of microbiome datasets focuses on unveiling protein functional diversity. [Read More]

October 7, 2020

From Life at the Extremes to Editing Genomes

Jennifer DoudnaJennifer Doudna and Emmanuelle Charpentier were recognized for their work on CRISPR-Cas9, technology described by the Nobel Foundation as having “a revolutionary impact on the life sciences.” For the past few years, Doudna’s lab has partnered with JGI’s Microbiome Data Science group led by Nikos Kyrpides, mining the IMG/M system for novel Cas genes and CRISPR systems. [Read More]

August 30, 2013

Subsurface Sediment Yields Novel Organism

Metagenomic analysis emphasizes the “extraordinary microbial novelty” of poorly-explored subsurface ecosystems The Science Through metagenomics, researchers reconstructed a dominant organism and member of a new phylum-level lineage from an aquifer sediment in Colorado. The Impact Analysis of the complete microbial genome led to a detailed metabolic model with evidence for multiple new enzymes and pathways…. [Read More]

July 22, 2013

Solving Microbial “Dark Matter” With Single-Cell Genomics

Microbes facilitate many of the natural cycles in plant growth and health, and play roles in  many processes in nutrient cycles that control certain environments and climates. Though thousands of these microbes have been identified, the majority of these microbes are still a mystery to scientists and are referred to as microbial “dark matter.” Steps… [Read More]

July 15, 2013

Microbial dark matter study in Nature

“This is an astounding paper,” says Norman Pace, a microbiologist at the University of Colorado–Boulder. “The achievement of hundreds of genome sequences from single cells at a shot is an entirely new level of microbiology.” Read more in Nature [Read More]

July 15, 2013

Microbial dark matter study in BBC News

“For almost 20 years now we have been astonished by how little there is known about massive regions of the tree of life. This project is the first systematic effort to address this enormous knowledge gap.” – Phil Hugenholtz, director of the Australian Centre for Ecogenomics at the University of Queensland, in Australia Read more in… [Read More]

May 24, 2013

Microbial genomes help propose phylum name

Metagenomicsand single-cell genomics are tools helping researchers learn more about the “biological dark matter” that has not been cultivated and studied in the laboratory. In an article published May 14, 2013 in Nature Communications. [Read More]

May 10, 2013

A new technique for microbial genome assembly

The DOE Joint Genome Institute is also a national user facility focused on developing tools that more cost-effectively enable the assembly and analysis of the sequence that it generates. [Read More]

February 8, 2013

Student tools for hands-on genomics and bioinformatics lessons

Driven in part by the increased emphasis to give life sciences students hands-on experience in “real research,” the DOE Joint Genome Institute’s Genomics and Bioinformatics Education Program developed a series of educational modules for undergraduate programs to explore and annotate publicly available microbial genome datasets. Known collectively as the Integrated Microbial Genomes Annotation Collaboration Toolkit… [Read More]

December 3, 2012

Cheryl Kerfeld on IMG-ACT in The Scientist

  “Bioinformatics has become such an integral part of research. And being able to do this, to use these tools in an informed way and in a way that’s somewhat discerning . . . is really important,” explains Cheryl Kerfeld, director of the Genomics and Bioinformatics Education Program at the Department of Energy’s Joint Genome… [Read More]
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