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Robin Rohwer

@robinrohwer.bsky.social

880 followers 610 following 150 posts

Microbial ecology and evolution. Special love for freshwater lakes & long-term time series 🌊🌊🌊 ➡️ ⏳⏳⌛ ➡️ 🧬🖥️ ➡️ 📈📊📝 postdoc @ UT Austin working remotely from the Pacific Northwest (views my own) robinrohwer.com

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Robin Rohwer @robinrohwer.bsky.social · 24d

Just noticed the Q&A comment boxes on peerJ articles now- wow! neat idea, curious if they'll be used

Robin Rohwer @robinrohwer.bsky.social · Sep 8

I dunno, yes you can dig for it, but does anyone actually? Like actually click through *all* old versions of a preprint to check for comments???

Biorxiv reviews just feel like reviewing into the void- public doesn't notice them, authors can ignore/bury them, now we learn even authors don't see it?

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Robin Rohwer @robinrohwer.bsky.social · Sep 8

Missing from this discussion is that if authors want to bury a comment they don't like on their biorxiv preprint, all they have to do is just upload a new version. It happens even if they wanted it left in the public discussion, but want to address the comments with a new version!

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Robin Rohwer @robinrohwer.bsky.social · Sep 8

I was discouraged from giving biorxiv reviews when I realized they are buried as soon as a new version is posted.

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Robin Rohwer @robinrohwer.bsky.social · Sep 4

I think you should apply ;p After all it will fit "seamlessly into your existing commitments", and you've probably got an inside vote on the hiring committee

Robin Rohwer @robinrohwer.bsky.social · Aug 29

Pocket casts?

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Robin Rohwer @robinrohwer.bsky.social · Aug 28

It is really cool that V4-V5 captures organelles so well... but I LOLed a little when I realized JEDI was just new branding for good old v4-v5 16S primers

Robin Rohwer @robinrohwer.bsky.social · Aug 11

What's up with isme having uncorrected manuscripts up for months? How are papers "published in April" still not actually published? Since when was this a thing??

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Robin Rohwer @robinrohwer.bsky.social · Jul 14

Parallelle 😉

Robin Rohwer @robinrohwer.bsky.social · Jul 9

Another option in addition to sandpiper is IMNGS. Sandpiper searches NCBI metagenomes for markers, IMNGS searches NCBI amplicon datasets (and since you know the 16S... there are a lot more of those datasets out there)

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Robin Rohwer @robinrohwer.bsky.social · Jul 9

Ha cool. My first thought was a breast pump flange...ouch 😂

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Robin Rohwer @robinrohwer.bsky.social · Jul 1

I had to change pediatricians to do this.

I was met with derision when I asked about early vaccination. After seeing how parents are treated when requesting a "nonstandard vaccination schedule" I feel like I understand why parents become antivax.

A screenshot of the NYT article linked in the original post. In the "Consider early vaccination for children" section, the following is highlighted: "In the normal vaccination schedule, children who get the first M.M.R. at 1 get their second M.M.R. at 4 to 6 years, but in fact, children who have already had that first dose can get the second as early as 28 days after the first"

Robin Rohwer @robinrohwer.bsky.social · Jul 1

This is cool. Have long thought journal reviews/publishing should follow the WI DNR earn-a-buck model

Scott McGrath @smcgrath.phd · Jul 1

How to speed up peer review: make applicants mark one another

www.nature.com/articles/d41...

#AcademicSky

How to speed up peer review: make applicants mark one another

‘Distributed peer review’ of grants makes process more than twice as fast — and includes some cheat-prevention measures.

www.nature.com

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Robin Rohwer @robinrohwer.bsky.social · Jun 2

Congrats!! Well-deserved!

Robin Rohwer @robinrohwer.bsky.social · May 26

Yes but just not the type of coding the original post was using ggplot downloads as a proxy for.

Robin Rohwer @robinrohwer.bsky.social · May 26

Also lots of people code in python and then use ggplot to make their figures. And that's not what you mean when you say "coding in R" right?

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Robin Rohwer @robinrohwer.bsky.social · May 20

New swag from the @taccutexas.bsky.social machine learning training 😂

So nice to be back in Texas for a week, see my labbies IRL and learn some new things

Robin Rohwer @robinrohwer.bsky.social · May 14

Why did I study bacterial evolution when I could have studied pasta evolution? 🍝🤤

Imagine the fieldwork...

Nate Jacobs @nacobs.bsky.social · May 14

As an introdcution to the phylogeny of filled pasta paper: link.springer.com/article/10.1...

Evolution of the Italian pasta ripiena: the first steps toward a scientific classification - Discover Food

In this study, phylogenetic and biogeographic methods are used to investigate the evolutionary relationships between various types of Italian pasta ripiena (filled pasta) and related representatives f...

link.springer.com

Robin Rohwer @robinrohwer.bsky.social · May 9

For the large fraction being lower, do you think that is because proportionally more euk reads in those metaGs?

Robin Rohwer @robinrohwer.bsky.social · May 7

Ahh thanks! Ok so yeah, def higher than 5% but I guess even with very carefully made mags I should not expect to get close to what I'm used to with water!

(And I do like your combined marker+mag approach for dealing with this too)

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Robin Rohwer @robinrohwer.bsky.social · May 7

Yes I did not see the mag coverage listed explicitly since they used marker genes for the diversity part. Suspect that number was less impressive?

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Robin Rohwer @robinrohwer.bsky.social · May 6

I realized I had no baseline for a sanity check! Does make you think about interpreting mag data differently by system though.

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Robin Rohwer @robinrohwer.bsky.social · May 6

Ok wow, thanks. I was thinking only ~5% was really bad! 😅
Used to wanting to see ~50% in lake water!!

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Robin Rohwer @robinrohwer.bsky.social · May 6

Ha yes, and can you ever assemble until saturation anyway?!

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Robin Rohwer @robinrohwer.bsky.social · May 6

What percent reads mapped to MAGs is "good" for soil or sediment samples?

is lower than water samples OK/expected due to more complex communities?

🙏
🖥️🧬 microbiome, metagenomics

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