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Nicholas Cooley @npcooley.bsky.social · Dec 7

Back on my bullshit.
(emailing ridiculous questions about edirect to the nlm support email at weird hours)

Reposted by Nicholas Cooley

MU-Peter Shimon 🀄️ @mu-peter.bsky.social · Apr 25

☀️ Fiat lux!

Evidence for a single origin of bioluminescence in Octocorallia and infers the age of occurrence to around the Cambrian era, approximately 540 Mya

Evolution of bioluminescence in Anthozoa with emphasis on Octocorallia 🧪
royalsocietypublishing.org/doi/10.1098/...

Phylogeny of Octocorallia with bioluminescent ancestral states. Newly time-calibrated tree adapted from McFadden et al. [19] using UCE data. Traits were defined as bioluminescent (species or genus-level record), non-bioluminescent (negative record) or unknown (no record). Taxon branches are colour coded based on known genus-level depth ranges (green, shallow < 200 m; purple, deep > 200 m; blue, shallow/deep range spans both). Ancestral depth range estimates are from electronic supplementary material, figure S4. The two major clades represent the orders Malacalcyonacea (purple) and Scleralcyonacea (pink).

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Nicholas Cooley @npcooley.bsky.social · Apr 16

We found ourselves wondering why some closely related genomes had very different rates of pseudogenization, and whether those rate differences were real or not. It turns out there was a whole lot to that story, and it's finally published!

Many purported pseudogenes in bacterial genomes are bona fide genes - BMC Genomics

Background Microbial genomes are largely comprised of protein coding sequences, yet some genomes contain many pseudogenes caused by frameshifts or internal stop codons. These pseudogenes are believed ...

bmcgenomics.biomedcentral.com

Nicholas Cooley @npcooley.bsky.social · Apr 12

Who has two thumbs and wasted almost a week of work because they forgot that the default genetic code wasn’t the bacterial genetic code?

This guy!

Nicholas Cooley @npcooley.bsky.social · Feb 21

For anyone interested, we’re hosting a special session on Scalable Analysis for Big Biological data at GLBio here in Pittsburgh this summer! I believe applications close this Friday! We’d love to hear your large scale compute stories!

https://www.iscb.org/glbio2024/programme-schedule/sabbd

Nicholas Cooley @npcooley.bsky.social · Jan 17

Doing bioinformatics work is basically just an endlessly repeating version of that Doctor Who meme where someone asks the Doctor ‘is 4 a lot?’ and he replies ‘Depends on the context!’ with new and exciting values and contexts.

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Nicholas Cooley @npcooley.bsky.social · Jan 17

They’re ok. You can treat them like holiday movies if you want.

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Nicholas Cooley @npcooley.bsky.social · Dec 25

Type 2 fun accomplished!

Triumph Completion notification for Solo-ing Warlord's Ruin in Destiny 2.

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Nicholas Cooley @npcooley.bsky.social · Dec 22

Is it well known how many people are actually using MGI sequencing? It is pretty sparse in SRA submissions, at least for prokaryotes.

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Nicholas Cooley @npcooley.bsky.social · Dec 14

People don’t know this? It was like the 3rd thing anyone ever told me about R.

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Reposted by Nicholas Cooley

Per-Ola Norrby @peonor.bsky.social · Dec 12

We need a chemist to work on high throughput synthesis at AstraZeneca in Gothenburg careers.astrazeneca.com/job/gothenbu...

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Nicholas Cooley @npcooley.bsky.social · Dec 7

Solidarity forever.

Spencer Ackerman @attackerman.bsky.social · Dec 7

Remember: the Washington Post union is asking us not to read, click, stream or otherwise engage with any Post journalism (which I will not call ‘content’) today so as to support their strike.

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Reposted by Nicholas Cooley

Marnix Medema @marnixmedema.bsky.social · Dec 5

We are looking for a new colleague to work on ML/AI in bioinformatics! Come join WUR Bioinformatics as assistant/associate professor in a wonderful scientific ecosystem. Please RT!
www.academictransfer.com/en/335162/as...

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Nicholas Cooley @npcooley.bsky.social · Dec 4

UwU

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Nicholas Cooley @npcooley.bsky.social · Dec 3

It’s usually easy for me to forget that I’m colorblind, but some things, like trying to find the red tabbed connectors for the lights on our Christmas tree, definitely remind me.

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Reposted by Nicholas Cooley

Jeremy Kamil @macroliter.bsky.social · Nov 21

🧪 3 tenure-track microbiome faculty job openings in Hawaii! 🌞 🏄🏽‍♀️ 🍄 🧫 🧬 🦃

Anthony Amend @fungaloha.bsky.social · Nov 20

Please spread the word about 3 tenure track, hard-money microbiome faculty positions. These are well-resourced, come with their own grants, few teaching requirements (but lots of opportunities), potential footprint in our marine lab.
www.schooljobs.com/careers/hawa...

Career Opportunities at the University of Hawai'i | University of Hawai'i

www.schooljobs.com

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Nicholas Cooley @npcooley.bsky.social · Dec 1

All the cool kids gild Dredgen.

Nicholas Cooley @npcooley.bsky.social · Nov 29

Staring blankly into the abyss when suddenly the abyss says snidely “I see you forgot to add a progress bar to this function.”

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Nicholas Cooley @npcooley.bsky.social · Nov 22

Back on my bullshit (submitting a couple thousand jobs on the first day of vacation, so I can neurotically check in on them when I’m supposed to be relaxing).

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Reposted by Nicholas Cooley

Kevin Verhoff @kevinverhoff.bsky.social · Oct 31

Happy Halloween!

Reminder to slow the F down if you’re driving today!

A chart showing the number of pedestrian deaths in the US by day of the year. There is a big spike, particularly for kids, on Oct 31st.

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Reposted by Nicholas Cooley

Curtis Suttle @virosphere.bsky.social · Oct 27

Please share: @UBCScience is searching for 15 TT faculty in diverse areas of expertise science.ubc.ca/about/careers. Included are 2 positions in Quantitative and Environmental Science as part of a hiring cluster for black faculty; you will join 6 current UBC faculty science.ubc.ca/blackscholars.

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Nicholas Cooley @npcooley.bsky.social · Oct 28

I e-mail then on a semi-frequent basis! They’ve been great for all kinds of questions!

Nicholas Cooley @npcooley.bsky.social · Oct 28

In hindsight, reading a grant review on a Saturday morning was not my best life choice.

Nicholas Cooley @npcooley.bsky.social · Oct 26

You could probably put something together using the ART simulator. It expects a genome-like unit as an input, but you could probably just hand it your long reads as though they’re contigs.

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