From QIIME to Oligotyping

From QIIME to Oligotyping

QIIME is one of the most widely-used pipelines among microbial ecologists to analyze their high-throughput sequencing data. The more people [...]

Oct 6, 2014
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Oligotyping and Alignment

Oligotyping and Alignment

Probably because the underlying logic behind oligotyping is remarkably different from the canonical approaches to demarcate high-throughput sequencing datasets, certain [...]

Sep 14, 2014
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Oligotyping in VirtualBox

Oligotyping in VirtualBox

Çağrı Ulaş, a second year computer engineering undergrad from Canakkale Onsekiz Mart University, Turkey, created an Arch Linux-based VirtualBox image [...]

Sep 2, 2014
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Installing the Oligotyping Pipeline

Installing the Oligotyping Pipeline

Installing the oligotyping pipeline on a MAC or a Linux computer is as easy as writing this command in the [...]

Aug 16, 2014
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On the Human Oral Microbiome

On the Human Oral Microbiome

We, which includes myself, Jessica Mark Welsh, Gary Borisy and Susan Huse, have done a comprehensive (re)analysis of the human oral [...]

Jun 25, 2014
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Frontiers in Microbiology Topic for Oligotyping

Frontiers in Microbiology Topic for Oligotyping

I am very delighted to announce that Frontiers in Microbiology is now hosting a research topic on oligotyping, which is [...]

Dec 12, 2013
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How to Oligotype: Best Practices

How to Oligotype: Best Practices

Oligotyping is a supervised method, which makes it a method that greets its users with a learning curve. To make [...]

Nov 4, 2013
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Methods paper is out!

Methods paper is out!

The methods paper for oligotyping appeared in Methods in Ecology and Evolution: It was somewhat cumbersome to decide which journal [...]

Oct 16, 2013
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Network Analysis of Human Oral Microbiome

Network Analysis of Human Oral Microbiome

Bar charts, pie charts, NMDS plots, dendrograms are all nice, but I like exploring new ways to visualize complex data. [...]

Mar 29, 2013
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Sewage reflects the distribution of human faecal Lachnospiraceae

Sewage reflects the distribution of human faecal Lachnospiraceae

The paper that has the same title with this post is recently appeared in the journal Environmental Microbiology by Sandra L. [...]

Feb 28, 2013
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A Bacteroides Story in 30,000,000 Illumina reads

A Bacteroides Story in 30,000,000 Illumina reads

A while ago Jeff Gordon and his group published a manuscript, “Human gut microbiome viewed across age and geography“; a [...]

Feb 4, 2013
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Basic Sample Mapping with Oligotyping

Basic Sample Mapping with Oligotyping

Oligotyping pipeline generates all necessary files the user may need to investigate the distribution of the recovered oligotypes among their [...]

Feb 4, 2013
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A Walkthrough: Oligotyping Interface on VAMPS

A Walkthrough: Oligotyping Interface on VAMPS

VAMPS is now offering an oligotyping interface, which means, you can run oligotyping on publicly available datasets or datasets you uploaded [...]

Sep 17, 2012
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STAMPS Course at the Marine Biological Laboratory

STAMPS Course at the Marine Biological Laboratory

The MBL Course, “Strategies and Techniques for Analyzing Microbial Population Structure“, aims to “promote dialogue and the exchange of ideas [...]

Aug 1, 2012
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Oligotyping Pipeline Explained

Oligotyping Pipeline Explained

This document is an attempt to explain software pipeline for oligotyping. Please do not hesitate to ask any questions you [...]

May 11, 2012
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A Success Story: Gardnerella vaginalis Profiles Among Sexual Partners

A Success Story: Gardnerella vaginalis Profiles Among Sexual Partners

In this post you will read about the result of an oligotyping analysis that highlights the sexual tranmissibility of Gardnerella [...]

May 2, 2012
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Hello World!

Hello World!

I am a post-doctoral scientist in Marine Biological Laboratory, working under the supervision of Mitchell L. Sogin. And this is [...]

Feb 14, 2012
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