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Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials
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John Vogel
Dr. Vogel joined JGI in 2014 to establish a plant functional genomics program. Prior … switchgrass transformation pipeline and, in collaboration with industrial partners, generated hundreds of transgenic … et. al. 2014 Genome Diversity in Brachypodium distachyon : Deep Sequencing of Highly Diverse Inbred Lines 2014 Plant …
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JGIota: Looking Back at How Cow Rumen Samples Landed on a Syllabus
Back in 2011, JGI-supported researchers published a paper in the journal Science . It detailed how they’d used metagenomics to identify over 27,000 microbial genes. The data from that study is now used …
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SPRUCE-ing Up Science
Oak Ridge, Tennessee. Recently, Lawrence, in collaboration with researchers from ORNL, Lawrence Berkeley National … When Lawrence embarked on his PhD program at UC Merced in 2013, this field was just beginning to develop and expand … they worked to develop a tool that leveraged machine learning to help users determine which computer program …
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Computationally Classifying Fungal Lifestyles
Machine learning methods were applied on sequenced fungal genomes to … crops and feedstocks for biomass and biofuel production. Learning about the ecology and evolution of  Dothideomycetes … (green). (From Haridas S et al.  Studies in Mycology , 2020.) Using whole genome data from newly sequenced genomes, …
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JGI Advisory Committees Code of Conduct
… we nurture in our workplace and seek to establish with our stakeholders. In working toward a shared vision with members of the JGI advisory committees, we welcome and … duration of your service: Be engaged and responsive; Behave with respect and civility in all discussions and debate; …
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iPHoP: A Matchmaker for Phages and their Hosts
… these hosts are microbes like bacteria, not humans. With metagenomic sequencing, researchers have found more of … together into the same workflow, then uses a machine-learning model to give its integrated prediction a … pairs to generate a matrix of data points.  Applied to 216,015 high-quality virus sequences in the IMG/VR database, …
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Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
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ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
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BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly
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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
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Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics
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