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Toward More Reproducible, Reusable Stable Isotope Probing Experiments
… As SIP experiments shed more light on microbial communities than ever before — especially with the prospect of meta-analyses boosted by AI and Machine Learning — JGI … you are now enabling these much larger comparisons down the line,” Malmstrom said. In addition to improving …
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JGI Scientists Pen Genome Watch Articles
… Tanja Woyke and other JGI researchers made their debut … more to come in 2020. Researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office … first draft. Woyke has so far selected the authors of these pieces to represent diversity in research area, gender, as …
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Fishing for Novel Cellulose Degraders
… A “bait and hook” single-cell genomic approach to bioprospecting. The Science One of the most vital pieces of equipment for fly fishing is a boxful of lures. … The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science …
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A Complex Confection Decoded: Sugarcane Reference Genome
… Sugarcane was the last major crop without a reference quality … most harvested crop by tonnage, sugarcane accounts for 80% of global sugar production. A reference genome for the … challenging and took more than a decade because there were pieces from multiple boxes, including some duplicates, to …
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Iron-rich Microbial Mats’ Main Players: Marsarchaeota
… Novel archaeal lineage found in Yellowstone may have been … early Earth conditions. The Science Through a combination of sequencing tools and techniques applied to samples … of copies of a particular DNA sequence from just a few pieces of DNA. Summary The extreme environments found in …
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GenomeOcean Leverages AI to Decode Nature’s Secret Language
… Trained on environmental data, a new JGI tool more accurately … genome discoveries. Unlocking the intricate details of life’s genetic blueprint has long been a significant … As of June 2025, Genome Ocean was ranked the No. 1 most-downloaded genome foundation model on the huggingface …
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Exploring and Thinking Critically about Scientific Problems with JGI Interns
… While summer interns at the JGI from multiple programs had their own goals to achieve, they constantly collaborated with each other on new ways of presenting and researching science. …
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A Natural Mechanism Can Turbocharge Viral Evolution
… Understanding how a fundamental mechanism of evolution allows microbes to adapt to changing … a JGI bioinformatics research scientist, found that pieces of viruses with DGRs were found, on average, in … The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the …
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Defining a Pan-Genome for Antarctic Archaea
… Analysis of haloarchaeal metagenomes broadens understanding of … gene transfer mechanisms involved significant sized pieces.  Interestingly, much of the strain variation … This work was supported by the Australian Research Council … (project 4031). The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science …
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A Revamped Amplification Method that Enables Nearly Complete Single-Cell Genomes
… With a new methodology, scientists are now getting more complete … from single cells. The Science Studying the  genomes of microorganisms is incredibly useful for understanding the … up before sequencing, then computer algorithms stitch the pieces together and attempt to put them back into the …
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Mining Public Databases Yields Largest Map of Fungal Mitochondrial Genomes to Date
… By leveraging new tools and large-scale data mining, JGI researchers nearly tripled … genome data, unlocking new potential for AI-driven studies of energy metabolism. The Science Researchers produced … The work conducted by the U.S. Department of Energy Joint Genome Institute …
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Notes on the Microbial Diversity of Puerto Nuevo’s Coastline
… Puerto Nuevo is a small town along the Baja California coastline in Mexico. … UC Merced graduate student Sabah Ul-Hasan and alumnus of the JGI-UC Merced Genomics Internship Program, first …
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