Author Archives: Mark Christie

About Mark Christie

Mark Christie is an assistant professor in the Department of Biological Sciences and Department of Forestry & Natural Resources at Purdue University.

To review or not to review, that is the question

Imagine this scenario. You are industriously working away on your most recent paper (ignoring other pressing data analyses, administrative duties, and grant proposals). You have just begun to get into the zone of intense focus, writing nirvana, when DING!!! a … Continue reading

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Posted in career, peer review, science publishing | 3 Comments

Calculating genetic differentiation with R

As molecular ecologists, it is often necessary and useful to calculate some measure of genetic differentiation. This is often accomplished with metrics such as Wright’s Fst an or an unbiased analog (e.g., Weir & Cockerham’s Fst; G’st etc.). In addition … Continue reading

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Posted in population genetics, R, software | 13 Comments

Using GitHub with R and RStudio

A few weeks back, the Molecular Ecologist released an article about GitHub and also created an organization where you can fork or simply download code shared by the Molecular Ecology community. A few of you out there may still be … Continue reading

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Posted in bioinformatics, howto, R, software | 29 Comments

Homo sapiens: the unsung model species of molecular ecology

This week I’ve invited a good friend and fellow Homo sapiens, Jacob Tennessen, to contribute a guest post to the Molecular Ecologist.  Jacob is a Postdoctoral Scholar at Oregon State University, where he currently works with Mike Blouin and Aaron … Continue reading

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Posted in Uncategorized | 6 Comments

How to Backup and Store your Next-Generation Sequencing (NGS) data

Congratulations!  You have recently received a file path to retrieve your hard-earned next-generation sequencing data.  You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your … Continue reading

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Posted in bioinformatics, data archiving, genomics, howto | 1 Comment

Increasing productivity in an increasingly productive world

One of the things I have been thinking about lately is how to further increase my own productivity.  Regardless of your career goals, increasing your productivity is only going to help you accomplish more (by definition) and increase your esteem … Continue reading

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Posted in blogging, career, Uncategorized | 3 Comments

Q&A: Julian Catchen helps us dig into STACKS – Part II

As promised, below is part II of our interview with Julian Catchen. These questions focus more on the specifics of using stacks (i.e., user-related questions). Please see the first post if you are interested a general overview. Even more information, … Continue reading

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Posted in bioinformatics, genomics, howto, interview, methods | Tagged | Leave a comment

Q&A: Julian Catchen helps us dig into STACKS

Julian Catchen is a post-doctoral researcher at the University of Oregon, where he uses computational solutions to facilitate the analysis of next-generation sequencing data. Prior to obtaining his PhD, Julian worked for both Intel and IBM, experiences that no doubt … Continue reading

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Posted in bioinformatics, genomics, howto, interview, methods | Tagged | 2 Comments

Fear and loathing in academia – Getting the right kind of mentorship

This week I’ve invited a friend and colleague, Hayley Lanier, to contribute a guest post to the Molecular Ecologist.  Hayley is a Postdoctoral Fellow at the University of Michigan, where she works with Lacey Knowles.  She has contributed an excellent … Continue reading

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Posted in career, howto | 3 Comments

STACKS: A program for identifying and genotyping loci with next-generation sequencing data

If you have recently collected or are in the process of collecting next-generation sequencing data, then you may be wondering what the next step to working with your data will entail.  Hopefully, you have been working a little bit with … Continue reading

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Posted in methods, next generation sequencing, population genetics, software | Tagged , , | 2 Comments