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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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    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)
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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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    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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    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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    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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    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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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: Nikos Kyrpides

Content Tagged "Nikos Kyrpides"

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October 27, 2010

JGI-Murdoch University rhizobial project

Rhizobia are soil bacteria that can form a symbiotic relationship with legumes such as common domesticated crops such as peas, beans or clovers. These symbiotic bacteria fix atmospheric nitrogen inside nodules formed on the legume roots contributing around 65% of the nitrogen currently used in agricultural production. A joint venture has been established between the… [Read More]

June 28, 2010

DOE JGI’s role in managing Human Microbiome Project data on redOrbit

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]

June 28, 2010

DOE JGI’s role in managing Human Microbiome Project data on Medical News

“The HMP project catalog is a unique worldwide resource,” says molecular biologist Nikos Kyrpides of Berkeley Lab’s Genomics Division, who heads the Genome Biology and Metagenomics Programs for the Joint Genome Institute (JGI) and is the co-principal investigator of the DACC. “It has a central role in the HMP, not only in maintaining the list… [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]

May 26, 2010

GenePRIMP QC tool on Genetic Engineering & Biotechnology News

The program, said Pati, identifies gene-calling errors such as potentially incorrect gene start and end positions, large overlaps between genes, fragmented genes and missed genes. Gene-calling errors, noted Pati, can range from two percent to as much as 30 percent of the original genes identified in the genome and are dependent on many factors, such… [Read More]

May 26, 2010

GenePRIMP QC tool on PhysOrg

“There are a lot of different tools used for predicting genes in prokaryotes,” Kyrpides said. “The major problem we have is that they all produce very variable results. This impedes our ability to compare genomes sequenced and annotated from various sources, as they use different tools for gene prediction. GenePRIMP is not substituting any of… [Read More]

May 26, 2010

GenePRIMP QC tool on redOrbit

“With GenePRIMP we have achieved a major breakthrough in the improvement of the quality of structural annotations such as gene predictions,” said Genome Biology Program head and study senior author Nikos Kyrpides. He pointed out that using GenePRIMP offers researchers three major advantages: high quality results with reduced errors; an approach that can be used… [Read More]

May 26, 2010

GenePRIMP QC tool on ScienceDaily

Pati said GenePRIMP significantly reduces the amount of time scientists spend checking the whole genome by specifically highlighting errors that need to be manually corrected.  Read more on ScienceDaily. [Read More]

May 26, 2010

GenePRIMP QC tool on Medical News Today

More than a thousand microbial genomes have been sequenced at various sequencing centers in the past 15 years to better understand their roles in tasks ranging from bioenergy to health to environmental cleanup.  Read more on Medical News Today. [Read More]

May 26, 2010

GenePRIMP QC tool on EurekAlert

To assist in checking the quality of the microbial genomic DNA sequences generated before they are submitted to the federally funded public archive GenBank, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has introduced a quality control tool known as the Gene Prediction IMprovement Pipeline or GenePRIMP. GenePRIMP is described in a paper… [Read More]
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