Category Archives: methods

What is DAS? A new tool to recover genomes from metagenomes

There are a lot of data out there, and if you haven’t already noticed the ‘omics train has steadily stayed its path through the fruitful (but challenging) world of metagenomics. Metagenomics offers the chance to unravel complex microbial communities without … Continue reading

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Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, next generation sequencing | Tagged , , , | Leave a comment

Best practices in sample naming

Wherein I try to save me from myself Let’s imagine a young scientist, bursting to the seems with enthusiasm and schemes to uncover the secrets of the biological world. Everything is new and she learns as she goes! Let’s call … Continue reading

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Posted in data archiving, fieldwork, howto, methods | Tagged , | 1 Comment

Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies

Everything is meta these days – metabarcoding, metagenomics, and now meta blog posts that are reviews of reviews. Much like every ecologist at least dabbles in the molecular world, so most of those predisposed to molecular ecology and population genetics … Continue reading

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Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics | Tagged , , , , , , , , , , | Leave a comment

Retrieving a million sequences and avoiding primer bias, a new method that might have it all

We have come a long way since the early days when sequencing was a breakthrough method initially used to identify uncultured microbes from the environment. It is now been almost three decades, in fact, since the first microbial 16S rRNA … Continue reading

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Posted in bioinformatics, evolution, metagenomics, methods, microbiology, next generation sequencing | Tagged , , | Leave a comment

We have the technology. Is sequencing getting better, smaller, faster?

Okay, I know some version of the phrase “recent developments in rapid and affordable sequencing have made blah blah blah possible…” is something you’ve probably read 10,000 times. However, third-generation sequencing platforms have turned out to be pretty darn astounding. … Continue reading

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

Of Of Mice and Men: High school English class lives on in scientific paper titles

Writing titles for scientific papers is hard. The title is the one element of the paper everyone reads if they so much as skim a journal’s table of contents e-mail. These days, you also want something that’ll fit in a … Continue reading

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Posted in just for fun, methods, science publishing | Tagged , , , , , , , | 3 Comments

On hyRAD-X, another option for museum genomics

Last year, I profiled Suchan et al.’s “hyRAD” method for reduced-representation genome sequencing of degraded sources of DNA using RAD probes. While it’s too early to say whether hyRAD will be widely used by molecular ecologists looking to integrate historic … Continue reading

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Posted in genomics, methods, natural history, next generation sequencing, phylogenetics, phylogeography, population genetics, RNAseq, selection, transcriptomics | Tagged , , , | Leave a comment

(Un)usual sources of ancient DNA

Working with ancient DNA can be quite painful at times, but hard work pays off (or so they say) and scientists are starting to reap great benefits from their effort by exploring more and more things to extract DNA from.

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Posted in evolution, genomics, methods, Paleogenomics | Tagged , , , | 2 Comments

To RADseq or not to RADseq?

It’s a cliche to say that we live in a moment of unprecedented possibility for molecular ecology, as high-throughput sequencing methods drive the cost of collecting DNA sequence data ever lower. But at the same time, it’s a tricky moment, … Continue reading

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Posted in adaptation, association genetics, genomics, methods, next generation sequencing, selection | Tagged , , , , | 8 Comments

Dishing out Art: “Soiling” our microbiology curriculum

Sarah Adkins wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. She is a MS student working with Dr. Jeffrey Morris at UAB. They are looking at how microbes (i.e., phytoplankton and E. … Continue reading

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Posted in blogging, Coevolution, evolution, methods, microbiology, natural history, selection | Tagged , , , , , | Leave a comment