Category Archives: genomics

Visualize your genome assemblies

Posted on 18 Dec, 2017 by Elin Videvall

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily), is a program that creates visualisations of sequence assemblies that you can interact with. When assembling a genome with your favorite assembler, you are usually building graphs, from which … Continue reading →

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Diving deep: Exploring microbial communities under the seafloor

Posted on 7 Dec, 2017 by Kelle Freel

As we all sat staring at three large monitors in the front of the room, the remotely operated vehicle (ROV) Jason hung on to a borehole observatory with one hydraulic arm as the other arm plugged our sampling equipment into … Continue reading →

Posted in bioinformatics, community ecology, fieldwork, genomics, metagenomics, microbiology, transcriptomics | Tagged , , , | Leave a comment

It's decorative gourd genetics season, muppet-huggers

Posted on 8 Nov, 2017 by Jeremy Yoder

It’s the first week of November, and we’re at Peak Pumpkin. Jack o’lanterns are passé, but Thanksgiving (in the U.S.) and traditional winter-solstice-adjacent holidays will keep pumpkin pie and its infamous espresso-based brethren in style for almost two more months. … Continue reading →

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Star Trek Discovery made a debunked genome sequence into a plot point — but that’s not nearly the worst biology goof in the franchise

Posted on 22 Oct, 2017 by Jeremy Yoder

Anyone who’s been anywhere near my Twitter feed in the last month knows I’m pretty darned happy with Star Trek: Discovery, the latest iteration of the five-decade-old science fiction franchise. Discovery manages to build something new with the key elements … Continue reading →

Posted in bioinformatics, genomics, horizontal gene transfer | Tagged , | 3 Comments

Population genomics finds veritas in the demographic history of vino

Posted on 17 Oct, 2017 by Jeremy Yoder

One of the more, hah, fruitful applications of genomic data has been in crop and livestock improvement. Biologists know that domesticating plants and animals for human use has involved powerful artificial selection — usually inadvertent at first, then intensive and … Continue reading →

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

Posted on 21 Sep, 2017 by Kelle Freel

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 →

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

GeOMe aims to organize the "what, where, and when" of molecular ecology

Posted on 31 Aug, 2017 by Jeremy Yoder

This post is a guest contribution by Michelle R. Gaither, Eric Crandall, and Cynthia Riginos, collaborators on the GeOMe project. Many molecular ecologists spend weeks or even months in the field each year collecting samples for molecular analysis. Even before … Continue reading →

Posted in community, data archiving, genomics | Tagged , , | 3 Comments

Experimental harvesting reduces gene expression variation

Posted on 10 Aug, 2017 by Reid Brennan

Human activities represent unique selective pressures for natural populations. This is especially true for fish species where we routinely harvest individuals from the wild, i.e., through fishing. It has been recognized for some time that overfishing can result in population … Continue reading →

Posted in adaptation, conservation, evolution, genomics, transcriptomics | Tagged , | 1 Comment

Non-model organisms are so hot right now

Posted on 4 Aug, 2017 by Kelle Freel

What makes a model organism? Well, as the name suggests, they are widely studied and have been adapted to a vast array of common genetic techniques. A few of the most often utilized organisms, which you are most likely already … Continue reading →

Posted in bioinformatics, domestication, evolution, genomics, next generation sequencing, yeast | Tagged , | 1 Comment

The largest mammalian genome is not polyploid

Posted on 24 Jul, 2017 by Bryan McLean

Some 40 million years ago in South America, following the arrival of the common ancestor of caviomorph rodents from the Old World, big changes were afoot. Specifically, the caviomorph colonists were beginning to give rise to an extant evolutionary progeny … Continue reading →

Posted in adaptation, bioinformatics, genomics, RNAseq, transcriptomics | Leave a comment