Blog Archives

Mycoplasma Contamination in Cell-Line Based Experiments

May 6, 2014
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Mycoplasma Contamination in Cell-Line Based Experiments

For a few years now, my EvoSTAR colleague, Bill Langdon, has been exploring the degree to which Mycoplasma bacteria have contaminated experimental systems and even "infected" online databases with the contents of their genomes.  He and his colleag...

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Russ Altman’s Translational Bioinformatics Year in Review

April 22, 2014
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Russ Altman’s Translational Bioinformatics Year in Review

A few weeks ago the 2014 AMIA Translational Bioinformatics Meeting (TBI) was held in beautiful San Francisco.  This meeting is full of great science that spans the divide between molecular and clinical research, but a true highlight of this meetin...

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There is no Such Thing as Biomedical "Big Data"

February 11, 2014
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There is no Such Thing as Biomedical "Big Data"

At the moment, the world is obsessed with “Big Data” yet it sometimes seems that people who use this phrase don’t have a good grasp of its meaning.  Like most good buzz-words, “Big Data” sparks the idea of something grand and complicated...

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More SOTU Scaling

January 30, 2014
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More SOTU Scaling

A couple of days ago the Monkey Cage featured Ben Lauderdale’s one-dimensional scaling model of US State of the Union addresses. In this post, I replicate the analysis with a closely related model, ask what the scaled dimension actually means, and consider what things would look like if we added another one. The technical details […]

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Using Database Joins to Compare Results Sets

November 20, 2013
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Using Database Joins to Compare Results Sets

One of the most powerful tools you can learn to use in genomics research is a relational database system, such as MySQL.  These systems are fairly easy to setup and use, and provide users the ability to organize and manipulate data and statistical...

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A Mitochondrial Manhattan Plot

November 6, 2013
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A Mitochondrial Manhattan Plot

Manhattan plots have become the standard way to visualize results for genetic association studies, allowing the viewer to instantly see significant results in the rough context of their genomic position.  Manhattan plots are typically shown on a l...

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Call them what you will

October 28, 2013
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I’ve been playing around with the R package texreg for creating combined regression tables for multiple models. It’s not the only package to do that – see here for a review – but it’s often handy to be able to generate both ascii art, latex, and html versions of the same table using almost identical […]

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Damaged and can’t be opened

August 13, 2013
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Perhaps you tried to open some application or mount some DMG on your Mac and encountered the following alarming message “[Application] is damaged and can’t be opened. You should move it to the trash.” Perhaps it is indeed damaged. But more likely it is just not signed by its developer or not made available from […]

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Understanding the ENSEMBL Schema

August 12, 2013
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Understanding the ENSEMBL Schema

ENSEMBL is a frequently used resource for various genomics and transcriptomics tasks.  The ENSEMBL website and MART tools provide easy access to their rich database, but ENSEMBL also provides flat-file downloads of their entire database and a publ...

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EPSA 2013 Programme

June 15, 2013
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If you are planning to attend the European Political Science Association (EPSA) meeting in Barcelona next week you might find a searchable online programme helpful (scraped out of the original pdf).

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