Author Archives: Chris Mason

Culture Methods

One of the current challenges in metagenomic studies and relying on sequence data is to determine whether the organisms you characterize are alive or not. Indeed, just finding DNA of Staphylococcus aureus on a wooden bench or subway pole doesn’t mean the organism is alive. Thus, to supplement our metagenomic profile of the subway system […]

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Run the PathoMap Human Ancestry Pipeline on Arvados!

Introduction PathoMap started with a simple idea; can we collect and study DNA from the New York City subway stations? We soon found the answer to be “yes!” And so we began to create a to do list: Collect samples from all 468 stations………………………Complete Extract DNA from all samples………………………………..Complete Prepare libraries and sequence samples……………………Complete Classify […]

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The long road from Data to Wisdom, and from DNA to Pathogen

I. Introduction There is an oft-cited hierarchy for data, wherein ideally it should flow: Data –>Information –>Knowledge –>Wisdom (DIKW).  Just because you have data, it takes some processing to get quality information, and even good information is not necessarily knowledge, and knowledge often requires context or application to become wisdom. For example, you could have […]

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Donate to PathoMap!

We need you to help keep the science going! To make a tax deductible donation to Weill Cornell Medical College to support the PathoMap project, please click here Or Donations can be mailed to: Weill Cornell Medical College Office of External Affairs 1300 York Avenue, Box 314 New York, NY  10065 Phone:  646-317-7427 or toll […]

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A day in the life of the Penn Station microbiome

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To gauge the persistence of a microbial signature at a station, we sampled one train station (Penn Station) in triplicate every hour on the hour during a weekday. We found that certain taxa are prevalent at every time point, yet a high degree of fluctuation was observed in some genera over the course of the […]

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The elusive bacteria of the South Ferry station

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The station with the most unique bacteria was the South Ferry Station on the ‘‘1’’ subway line in Manhattan. This was the only station completely flooded during Hurricane Sandy in 2012, and it has been closed since that time. Notably, we observe ten unique species of bacteria that were present in the single flooded station […]

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