David Koslicki Website

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Nature paper picked up in news outlets

Article

The Nature Translational Psychiatry paper has been picked up by a number of news outl
Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

publication

Friday, May 11, 2018

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.
Featured article in OSU iMPACT

Event

Tuesday, May 1, 2018

My recent work with the CAMI project was
NIH NCATS grant award

Article

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).
Improving Min Hash for Metagenomic Classification

publication

Tuesday, July 4, 2017

This work improves upon the so called "min hash" technique (a "probabilistic data analysis" method) to develop a very fast and efficient way to estimate the similarity of two sets of objects (in terms of how much they overlap). The approach we present is orders of magnitude faster (and uses orders of magnitude less space) when two data sets under consideration are of very different size. The kinds of sets we consider are sets of sub-strings (called k-mers) of DNA sequences from communities of microorganisms.

Nature paper picked up in news outlets

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

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

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

Featured article in OSU iMPACT

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

My recent work with the CAMI project was featured in the OSU iMPACT magazine. 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

NIH NCATS grant award

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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