Author Archives: Noah Snyder-Mackler

What do with all those pesky mtDNA reads in your NGS experiment

Posted on 21 Jul, 2015 by Noah Snyder-Mackler

Have you ever noticed how many reads from your high throughput sequencing project map to the tiny fraction of your genome that is the mitochondrial genome (mtDNA)? Pretty much any NGS experiment (e.g., RNA-seq, DNA-seq, capture-based sequencing) leave you with … Continue reading →

Posted in bioinformatics, genomics, howto, mutation, software, Uncategorized | Tagged , | Leave a comment

Raising the NIH pay-line to 20%

Posted on 14 Jul, 2015 by Noah Snyder-Mackler

I bet that title got your attention. In the good ol’ days our funding record made the United States look like the land of milk and honey. As Bruce Alberts’ and colleague wrote in PNAS earlier this year: “The United … Continue reading →

Posted in career, funding, NIH, politics, United States | Tagged , , , | Leave a comment

Mixed modeling of methylation measures (increase your power by 60%)

Posted on 7 Jul, 2015 by Noah Snyder-Mackler

Do you want to increase your power to detect differentially methylated CpG sites by 60%*? Yes?! Then do I have the pre-print for you.

Posted in bioinformatics, genomics, methods, next generation sequencing, software | Tagged , , | 1 Comment

The genomics of bee sociality

Posted on 27 May, 2015 by Noah Snyder-Mackler

Bee species cover the spectrum of sociality: there are solitary bees, there are eusocial bees – which are divided into facultative eusocial (the ones that can be either solitary or eusocial depending on external cues) and obligate eusocial bees, and … Continue reading →

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Getting swole with Burmese pythons: the transcriptomics of python feeding

Posted on 19 May, 2015 by Noah Snyder-Mackler

Burmese pythons can get pretty big. And they get even bigger after they eat a meal: like a mouse or an alligator. Indeed, their guts undergo rapid changes in form and function during and after a feeding bout. And, since … Continue reading →

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Another lesson in genomics experimental design and avoiding batch effects

Posted on 12 May, 2015 by Noah Snyder-Mackler

Twitter has been abuzz with Orna Man and Yoav Gilad’s (re)analysis of the data from a recent PNAS paper: “Comparison of the transcriptional landscapes between human and mouse tissues”. The PNAS paper concluded that the gene expression profiles of different … Continue reading →

Posted in bioinformatics, genomics, next generation sequencing, RNAseq | Tagged , , | 3 Comments

The death of the p-value? Probably not.

Posted on 5 May, 2015 by Noah Snyder-Mackler

In February, a social psychology journal, Basic and Applied Social Psychology , made the bold (and extreme) move to ban the use of p-values, F-statistics, T-values, and any other form of Null Hypothesis Testing (NHT) method. This major move generated … Continue reading →

Posted in methods, politics, science publishing | Tagged , , | 3 Comments

A mammoth bottleneck prior to extinction

Posted on 28 Apr, 2015 by Noah Snyder-Mackler

Here’s to back-to-back posts on extinct mammalian genomes! Woolly mammoth genomes are all the rage. How do I know? Just check out the new book, pre-print, and paper that were recently published.

Posted in conservation, genomics, next generation sequencing, Paleogenomics, population genetics | Tagged , , | Leave a comment

The gopher tortoise gut microbiome

Posted on 14 Apr, 2015 by Noah Snyder-Mackler

A few weeks ago I wrote about a study on socially structured gut microbiomes in wild baboons. Well, now I’m here to tell you about a new study that examined the population structure of tortoise gut microbiomes.

Posted in community ecology, genomics, natural history, next generation sequencing, population genetics, Uncategorized | Tagged , , | 1 Comment

A call for statistical editors in ecology

Posted on 7 Apr, 2015 by Noah Snyder-Mackler

A new article in TREE wants to add a specialized reviewer to the peer review process. von Wehrden, Schultner, and Abson suggest that a statistical editor would expedite* the peer review process: “The review process of a manuscript with imperfect … Continue reading →

Posted in Uncategorized | 3 Comments