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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    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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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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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)
    Streamlining Regulon Identification in Bacteria
    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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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    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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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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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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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    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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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    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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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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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: bioinformatics

Content Tagged "bioinformatics"

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]

July 3, 2012

Fungal genomics and coal formation in BioBased Digest

In Massachusetts, a group of 70 researchers led by David S. Hibbett of Clark University, in Worcester, Mass. and Igor V. Grigoriev of the Department of Energy’s Joint Genome Institute comparing the genomes of 31 fungi to determine how white rot fungi breaks down lignin and could be a major breakthrough in cellulosic ethanol technology. Read… [Read More]

June 28, 2012

Linking white rot fungi and the Carboniferous period in Scientific American

Now a new genomic analysis suggests why Earth significantly slowed its coal-making processes roughly 300 million years ago—mushrooms evolved the ability to break down lignin. “These white rot fungi are major decomposers of wood and the only organism that achieves substantial degradation of lignin,” explains mycologist David Hibbett of Clark University in Massachusetts, who led the research… [Read More]

May 26, 2012

Kbase and DOE’s Susan Gregurick in GenomeWeb’s BioInform

Kbase is currently in alpha release and is targeted for full production release in early 2013.The community-driven and scalable open-source system is intended to provide a framework for evidence-based functional annotation of genome sequences. It will also enable the creation of metabolic and regulatory models that may be used to generate scientific hypotheses; as well… [Read More]

March 9, 2012

Bioinformatics challenges for metagenomic analyses

There are more microbes in, on and around the planet than there are stars in the sky. However, the vast majority of these microorganisms have not yet been studied, in part because many of them do not thrive when moved out of their natural environment. A spoonful of soil contains a complex and diverse microbial… [Read More]

June 6, 2010

DOE JGI’s role in managing Human Microbiome Project data

At JGI, Kyrpides oversees projects such as GenePRIMP, a highly rated quality control program for genome sequencing, and GOLD, the Genomes On-Line Database. GenePRIMP stands for “Gene PRediction IMprovement Pipeline, and it consists of a series of computational units that can be used to significantly improve the overall quality of the predicted genes in any… [Read More]

April 5, 2010

Peach genome project on WSU Today Online

The International Peach Genome Initiative’s decision to release the genetic makeup of the peach ahead of publication in a scientific journal could have far-reaching implications for the future of peaches and related Rosaceae plants like almonds, blackberries, apples, cherries, plums, raspberries, roses, strawberries and trees such as poplar, citrus and chestnut. “Having access to even… [Read More]

August 10, 2009

JGI’s new head of informatics

Svilen Tzonev has been named head of informatics at Department of Energy’s Joint Genome Institute in Walnut Creek, Calif. He was formerly at Illumina, where he was the senior director of software, bioinformatics and IT and helped to develop and commercialize the Genome Analyzer system. Prior to that post, he was director of software and… [Read More]

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