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RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
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Natural Prodcast Episode 1: The Primer, Part 1
… DAN: You’re listening to the US Department of Energy Joint Genome Institute’s “Natural Prodcast,” a … – problems that might need special technology for DNA sequencing, genomics, metabolomics, and synthetic biology, … the JGI. And so now here at the JGI, I work with all of the sequencing data that the JGI produces to try to find and …
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Genome-wide role of codon usage on transcription and identification of potential regulators
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Tanja Woyke Awarded van Niel International Prize for Studies in Bacterial Systematics
… the van Niel International Prize for Studies in Bacterial Systematics for the triennium 2017-2020! Established by the University of Queensland in 1986, the van Niel Prize recognizes … of a panel of experts of the International Committee on Systematics of Prokaryotes. Due to the ongoing pandemic, …
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Natural Prodcast Episode 4: Nancy Keller
… DAN: You’re listening to the US Department of Energy Joint Genome Institute’s “Natural Prodcast,” a … out introns and dealing with, you know, weirdness in the sequence. You know, some clusters are not clustered…   … species”… he’s now found that some fungi have different ITS sequences in their genome, which might get you a little …
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Frequently Asked Questions: Proposal Submission
… See below for a list of Frequently Asked Questions about our proposal submission process. You can review successful letters of intent and submissions at the bottom of the page.  … Review the list of open calls ; click on the call link to see specific … supported, sample/capacity limits, and instructions.  Many of the submissions are done using web-based forms.   To view …
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Sequencing Technologies & Products
…   Our Sequencing Technologies Group is well-integrated across JGI departments to ensure a robust offering of sequencing capabilities and products to our users. This … technology has been further scaled to a multiplexed DAP-seq (multiDAP-seq) method allowing high-throughput …
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Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups
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DAP-seq Drives Robust Mapping of Gene Regulation
… Now, with improvements to DNA Affinity Purification Sequencing (DAP-seq), these barriers are falling. As  … of large plant genomes. In addition: Multiplexed barcoding enables the simultaneous profiling of multiple species; … high-quality single-nuclei transcriptomes, enabling the identification of dozens of unique cell types in plants such …
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Natural Prodcast Episode 3: The Primer, Part 3
… DAN: You’re listening to the US Department of Energy Joint Genome Institute’s “Natural Prodcast,” a … and the 90s. And so we started to be able to explore DNA sequencing and actually get to the DNA sequence – sequences for the genes that code for the … This the third episode of Natural Prodcast, and the third and final part of our …
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How to Submit Sequencing Samples
… Below is a brief description of the process needed to prepare and ship samples for sequencing by the JGI.  Additionally it includes … sample QC requirements and protocols Obtaining DNA and RNA of suitable quantity and quality has been the rate-limiting … material is one of the greatest predictors of a successful sequencing project. It is imperative that users properly …
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Examples: Successful LOIs & Submissions
… See below for examples of successful Letters of Intent to our Community Science Program Large-Scale Call, … Linking lignin engineering to drought stress resilience: RNA-seq and metabolomic insights in lignin biosynthetic pathway … to soil carbon storage during simulated range shifts of plant-fungal symbionts …
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