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  • Assessing taxonomic metagenome profilers with OPAL
    publication
    Monday, March 4, 2024

    We introduce a framework to compare tools utilized to determine what microbes are present in a sample, and at what relative abundance. This will help computational biologists design better tools to analyze communities of microorganisms (which affect nearly everything in existence!).

  • MiCoP: Microbial Community Pro ling method for detecting viral and fungal organisms in metagenomic samples
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    Thursday, November 1, 2018

    We show that read mapping, along with a probabilistic assignment of multi-mapped reads, outperforms other computational approaches to identify the presence and relative amount of viral and fungal organisms in a metagenomic sample of microorganismal DNA.

  • The Biomedical Data Translator Program: Conception, Culture, and Community
    publication
    Friday, November 9, 2018

    A description of the NIH NCATS culture that emerged during the Translator project.

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  • Toward A Universal Biomedical Data Translator
    publication
    Friday, November 9, 2018

    The vision and high-level overview of the NIH National Center for Advancing Translational Science (NCATS) project entitled "Translator" (through which we have been funded). The goal of the project is essentially to build a biomedical "Siri": an automated platform for answering biomedical research questions that leverages repositories of publicly available information.

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  • Blood microbiome research featured in The Oregonian
    Article

    The Oregonian (a Portland-based newspaper) has featured our work in analyzing the blood microbiome of patients with and without mental disorders.

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The Oregonian (a Portland-based newspaper) has featured our work in analyzing the blood microbiome of patients with and without mental disorders.

The feature can be found here: http://www.oregonlive.com/sponsor-content/?scid=135575&prx_t=chYEAmggrATQ4PA

  • Read more about Blood microbiome research featured in The Oregonian

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The Nature Translational Psychiatry paper has been picked up by a number of news outlets, including KTVZ (Oregon News Channel 21) and Reddit!

http://today.oregonstate.edu/news/schizophrenics%E2%80%99-blood-has-more-genetic-material-microbes

  • Read more about Nature paper picked up in news outlets

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Along with collaborators at UCLA, we were able to detect a small, but significant amount of microbes in blood This is surprising since it's typically assumed that the immune system typically removes any microbial presence from human blood. I used a reference-free microbial community algorithm, called EMDeBruijn, to help corroborate the patterns we saw which included an increase in microbial diversity in schizophrenia patients. EMDeBruijn is a metric based on the Wasserstein metric (aka the Earth Mover's Distance) and a de Bruijn graph induced by the k-mers in a metagenomic DNA sample.

  • Read more about Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

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Submitted by koslickd on Tue, 05/01/2018 - 09:10

My recent work with the CAMI project was 51网络优化专家|513网络优化专家 V8.0.2.2 绿色版 下载 ...:2021-11-30 · 513网络优化专家是一款绿色免安装的网络优化加速软件，软件全面覆盖国内的所有网游，能够有效解决用户在游戏中遇到的延时高、登录慢、掉线频繁等问题，给您一个舒适、流畅的游戏环境。 51网络优化专家 特点： 1.绿色免安装 2.全面覆盖国内所有网游，能有效解决您在网游中遇到的延时高 .... The article summarizes the results of the most recent CAMI challenge in which performed a large scale comparison of metagenomic analysis tools (and discovered that many do not perform as well as advertised).

  • Read more about Featured article in OSU iMPACT

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I'm pleased to announce that we've recently been funded by the NIH National Center for Advancing Translational Sciences (NCATS) along with Steve Ramsey (Oregon State). Co-PI subawardees include Eric Deutsch (ISB), and Arnab Nandi (Ohio State).

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  • Read more about NIH NCATS grant award

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