Showing posts from 2016

A list of interesting papers on optical mapping

At GYDLE inc., I work on optical mapping problems, and sometimes I find solutions to these problems. To tackle efficiently any problem, the error model for the problem must be understood. To write software that deals well with a given type of data, this type of data has to be understood, and one must be able to separate the good data from the bad data.

Once in a while, I read scientific papers to keep myself up to date with the optical mapping technologies. I created a Mendeley group where I maintain a list of papers on optical mapping. The list is available here. Some of these papers describe error models for optical mapping.

The Bioinformatics Adventure continues.

According to  the social network LinkedIn, I have been working on optical mapping problems at Gydle Inc. (with Philippe and Marc-Alexandre) for 8 months so far. I previously worked at Argonne National Laboratory (with Fangfang and Rick and other people).

The Bioinformatics Adventure continues. Yes, I am still doing bioinformatics. No, I no longer work on assemblers.

I have not worked on any genome assemblers for a while. As of now, I am more an aligner person than an assembler person (see "Sense from sequence reads: methods for alignment and assembly").

At Gydle Inc, we are 3 employees (the CEO, a computer scientist, and myself). Our CEO worked at Illumina at some point. Working in a small company is very fun. We get to do a lot of different things:

algorithm design,software design,software development,software quality control,test development, ticket management,data analysis,data curation.
I schedule my time around activities related to the development of optical mapping s…