Wow, I never really noticed this 'fastp' software. I'm apparently the only one though. They simply re-used an existing name already employed by popular and historically significant software. How is this kind of thing possible? academic.oup.com/bioinformati...

Here's a fun paper! The bibliography is fire. I wonder what they have to say about evolutionary genomics? eppd13.cz?page_id=2587

I totally agree with this approach. There's no real benefit to collecting replies from randos. I'm not Ash Ketchum and replies aren't Pokemón. I do not need to catch 'em all.

1/12 Excited to share our new paper. Many essential functions, like DNA packaging and chromosome integrity, are encoded in highly repetitive, "recalcitrant" parts of the genome. But these regions have been incredibly hard to study. Until now. genome.cshlp.org/content/35/9...

Fellow #Drosophila researchers! Ever wondered about the genome sequence of your lab strain or the balancers? Check out our Drosophila Laboratory Pangenome Database, featuring a growing collection of reference genome assemblies for popular D. melanogaster strains! github.com/chakrabortym...

Just remembering that for one of my PhD rotation projects in 2000, I explored using DHPLC for population genetics analysis in Drosophila. Hah, dodged a bullet there, eh? It turns out to have had a fairly short shelf life and was replaced by nextgen sequencing.

Huh, I have the inverse reaction. Private institutions aren't fundamentally pedagogically oriented these days. Rather the opposite really. State institutions have explicit, legislated pedagogical goals that aren't inherently in tension with maintaining endowment performance.

When selecting an Open Access publishing license, has the CC-BY versus CC-BY-NC ever mattered to run-of-the-mill publicly funded basic research where patents, commercialization and the like are non-issues? If so, which one is more desirable?

We were this close from Wikipedia hallucinations being fed into Google hallucinations. arstechnica.com/ai/2025/06/y...

This is horribly misguided. Preprints are nothing more than vehicles for disseminating work that is nominally unreviewed. Preprints don't serve an anti-science agenda outside of how they are employed. Scientists are already skeptical of journals they aren't familiar with. I don't see the difference.

"Patterns of crossover distribution in Drosophila mauritiana necessitate a re-thinking of the centromere effect on crossing over" Oh wow, THIS is what Scott Hawley and I exchanged some e-mails about last year! Definitely gotta read this now. academic.oup.com/genetics/adv...

Does anybody know if NIH advisory council meetings have resumed? I'm curious if the council meeting for NIGMS on February 6th will be held on Wednesday as scheduled?

So far, my most significant/consistent use of LLMs is to ensure my e-mail correspondence is polite and concise. I'm still not confident in doing more than experiment on using it for anything else. To be clear, I haven't coded too much lately, so maybe it will shine there when I get around to it.

Hello Bluesky friends! I am a #newPI starting at UC Irvine in April, interested in gene regulation and functional genomics in stem cell models of development (esp neural crest). We are hiring at all levels – please reach out/spread the word! sskimlab.org

I've come to view eLife's various initiatives as a reflection of the academic incentives familiar to its creators. The drive for "innovation" or a push to "experiment" with different models is what an academic scientist would do. And an academic scientist would also exaggerate just how novel...

Research is a conversation. Participants should listen as often as they speak. Unfortunately, we reward those who talk the most and the loudest, irrespective of how well they listen, or indeed whether they listen at all. In short, publish less, review more.

Many academics point to bioRxiv as “the one thing improving science publishing”. If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2

With the exception of the last clause, I wholeheartedly agree. However, haphazard engagement of preprinted material is not a reliable way to solicit peer engagement with scientific work. The preprints that receive substantive engagement are a small non-representative proportion of total work.

No more pencils, no more books, no more teacher's dirty looks!

My twitter account has been closed and locked since November 2022, but I had left the posts up until now. I just deleted the entire thing in 15 minutes, thanks to a great script from Luca Hammer: github.com/lucahammer/t... Thanks to @amyhoy.bsky.social and @thomasfuchs.at for steering me there.

I hate the Globus interface. That is all.

What is going on with follow requests lately? I think my follower count has doubled in the past few weeks alone. Don't get me wrong, it's great. But I can't even keep up with them all. Are other people also experiencing this? Platform tweak, exodus from the other place, both?

It's awesome to get a shiny new computer or laptop, but most of us dislike setting it up. What's the most useful setup task you always procrastinate on because you forgot how to do it since you only do it once when setting up a new system? For me, it has to be setting up ssh keys with my servers.

When do we acknowledge that the best way to mitigate some bad behaviors isn't through 20 minute online educational modules?

I used to get annoyed at bad behavior on social media. The "reply guys", trolls, engagement baiters, grifters, etc. drove me nuts*. But I also wanted the free wheeling conversations that an unfettered platform provides. I realize now that, even with blocking, muting, selective engagement, etc...

First they did a boxer, now they're doing whippets. www.biorxiv.org/content/10.1...

I am super pleased to announce that our NIH MIRA has been awarded! This grant will sustain our research on genome evolution. We're planning some exciting projects on population genetics and molecular evolution of structural variation. We're also delving into bioinformatics of these regions.

Counterpoint: You don't set an out of office reminder, aren't actually out of the office, and still never respond to e-mails. www.embopress.org/doi/full/10....

This is our latest foray into studying genetic variation in challenging parts of the genome that nevertheless encode important genes. We're very interested in what everyone thinks. One key realization we came to is that assembly isn't even the hardest part.

Ouerghi et al @docedge.bsky.social identify a serious flaw in the null hypothesis calculations of a new low-fold sequencing forensics id method. The mistake leads to match probabilities, which can be quoted in court, being off by orders of magnitude www.biorxiv.org/content/10.1...

Adriana Briscoe elected to NAS. news.uci.edu/2024/05/01/u...

📄 New publication from the lab! Are you interested in subfunctionalization of gene duplications? Immune gene evolution? Blood sucking insects? Then check this out! academic.oup.com/icb/advance-...

Interesting. The original form of what became the "two button meme" was actually pretty good to begin with. jake-clark.tumblr.com/post/1009467...

Hilarious. My partner just joined a (professional) conference call as the first caller. The hold music is Never Gonna Give You Up. I'm speechless.

Super scary. My partner's friend is experiencing a nightmare right now. Their family's identities were stolen over the weekend. Already, several credit cards, cars, and even a mortgage have been fraudulently obtained in their names. The attack was targeted during the weekend, when nobody is at work.

Some artist played a lot of Mario Bros. games. That Tesla is Mario at 2:06. www.youtube.com/watch?v=uylY...

Every once in a while, I'm reminded of a very special "Reviewer 2" who clung tenaciously to their opinions through three rounds of objections to our manuscript being published. Some of the comments were innocuously wrong, but funny, while others simply indicated being out of step with the field. 1/2

I'm teaching a two week stint in our graduate evolution reading class. I just returned from an invigorating #TAGC24, and I'm super excited to be back in the lab. I'm feeling a lot of that energy bleeding into the grad course. Looking forward to the next two weeks!

Public service announcement. This is how you search for exact phrases in macOS Preview. I have spent years not realizing how to do this I don't know when it switched from using quotes around the phrase to using this drop down option, but it's been years. If only I'd known sooner!

Each time I see one of these listicles, I look for Taipei's MRT and I'm always disappointed. It's genuinely great. Punctual, good coverage, fast, clean, and convenient. It's especially annoying when I see Chicago's "L" being represented. The MRT is so much better. www.cnn.com/travel/world...

More ChatGPT fun. Prompt: Please write a limerick about Galadriel's beauty from the perspective of Gimli, Son of Gloin. Response: In Lothlórien's woods so fair, Gazed Gimli with raptured stare. For Galadriel's grace, No dwarf could erase, Her visage beyond compare.

Last ChatGPT anecdote of the day. It steers clear of taboo topics but apparently loves dad jokes.

I've been chatting about D&D with an LLM.

I've been experimenting with UCI's institutional interface to ChatGPT. I threw several text-only multiple choice midterm questions from classes I teach in genetics and ecology & evolution. It turns out ChatGPT doesn't do so hot, even when the questions are basic. It got 3/7 questions wrong.

I'm reliving some moments from high school Spanish class with ChatGPT as my companion. One student in our class wasn't very attentive, and was wondering why we were learning the phrase "Long live the shoe!" So, I asked what ChatGPT thought of that phrase.

Tree sequences as a general-purpose tool for population genetic inference https://www.biorxiv.org/content/10.1101/2024.02.20.581288v1

Though long, I found this very interesting. youtu.be/3Acx_n2WfYM?...

Idea: Uni Admins should reward, rather than threaten, the folks who don't respond to "mandatory" cyber security training. Reasoning: They are the ones who are most resistant to social engineering.

I like to imagine grammar/spelling police happening upon Jeff's posts and feeling the self righteousness fade into confusion and finally petulant frustration.

Sometimes ads don't even make sense. What on earth is going on in this tableau? It looks like a young woman in judges robes is testifying? The gallery is filled with other people also in judges robes. A prominent American flag on wall in the back of the gallery has 14 stripes and 6 rows of stars.