Saturday, February 22, 2014

Modest Data Reported From Oxford Nanopore's Exciting MinION Sequencing Platform

The first data from Oxford Nanopore's promising MinION sequencing platform was released a couple of days ago.  The sequencing data was released at the Advances in Genome Biology and Technology Meeting in Florida, and was presented by Dr David Jaffe of the Broad Institute in Cambridge, MA.  The reported data is a bit underwhelming because it failed to live up to the goals set by the company a couple of years ago, and because it does not seem to offer anything new to the field of DNA sequencing.  Here I am briefly going to go over the way the MinION system works, how it is performing, and what we can possibly expect in the future.  I also have my sources below, so check those out for further reading.

Thursday, February 13, 2014

Microbial Biomarker Discovery and How to Properly Format Your Data (Lefse)

Biomarker discovery is a big part of medical research.  A biomarker is a clinical signal, like the presence of a gene in your genome or colonization of your lungs with a certain bacterial species, whose presence or absence indicates a disease state or predicts an increased risk for developing a disease state.  These play important roles in medicine because they can allow for disease diagnosis (ie. the physician can test for the disease biomarker) or provide a prediction of whether the patient is at a higher risk for developing a condition (ie. a gene that puts a patient at higher risk for developing diabetes).  There are some good programs out there for biomarker discovery, but one I particularly like is Lefse.

Tuesday, February 4, 2014

ReadCube: One Giant Leap for Sceintific Literature Management

Maybe you know the feeling?  A "scientific literature" or "articles" file with a confusing tree of sub-files that you need a map to navigate.  Hundreds of articles titled "Sci_paper01119922838347.pdf" that contain who-knows-what.  Constantly having to navigate your University's version of PubMed or Google Scholar whenever you need a new paper.