J.J. Emerson 艾偉傑 🖥️🧬
@jjemerson.bsky.social
📤 2041
📥 1041
📝 301
Evolutionary geneticist at UCI. JJ_Emerson on
http://ecoevo.social
.
Here's a fun paper! The bibliography is fire. I wonder what they have to say about evolutionary genomics?
eppd13.cz?page_id=2587
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The Specificity of the Hidden Defect in the Human Bio Element – EVROPSKÝ POLITICKÝ A PRÁVNÍ DISKURZ
https://eppd13.cz/?page_id=2587
5 days ago
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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.
add a skeleton here at some point
7 days ago
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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...
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Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
https://genome.cshlp.org/content/35/9/2023.short
11 days ago
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reposted by
J.J. Emerson 艾偉傑 🖥️🧬
about 1 year ago
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...
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GitHub - chakrabortymlab/DLPD: code and scripts relevant to the Drosophila Laboratory Pangenome Database
code and scripts relevant to the Drosophila Laboratory Pangenome Database - chakrabortymlab/DLPD
https://github.com/chakrabortymlab/DLPD
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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.
15 days ago
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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.
add a skeleton here at some point
21 days ago
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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?
4 months ago
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We were this close from Wikipedia hallucinations being fed into Google hallucinations.
arstechnica.com/ai/2025/06/y...
5 months ago
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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.
add a skeleton here at some point
7 months ago
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"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...
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Patterns of crossover distribution in Drosophila mauritiana necessitate a re-thinking of the centromere effect on crossing over
Abstract. We present a SNP-based crossover map for Drosophila mauritiana. Using females derived by crossing two different strains of D. mauritiana, we anal
https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyaf039/8063342
8 months ago
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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?
9 months ago
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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.
10 months ago
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reposted by
J.J. Emerson 艾偉傑 🖥️🧬
Seungsoo Kim
10 months ago
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
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Kim Lab at UC Irvine
Visit the post for more.
https://sskimlab.org
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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...
add a skeleton here at some point
10 months ago
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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.
10 months ago
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reposted by
J.J. Emerson 艾偉傑 🖥️🧬
Richard Sever
11 months ago
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
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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.
add a skeleton here at some point
11 months ago
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No more pencils, no more books, no more teacher's dirty looks!
11 months ago
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reposted by
J.J. Emerson 艾偉傑 🖥️🧬
Carl T. Bergstrom
about 1 year ago
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.
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GitHub - lucahammer/tweetXer: Delete all your Tweets for free
Delete all your Tweets for free. Contribute to lucahammer/tweetXer development by creating an account on GitHub.
https://github.com/lucahammer/tweetXer?tab=readme-ov-file
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I hate the Globus interface. That is all.
12 months ago
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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?
12 months ago
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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.
about 1 year ago
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When do we acknowledge that the best way to mitigate some bad behaviors isn't through 20 minute online educational modules?
about 1 year ago
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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...
about 1 year ago
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First they did a boxer, now they're doing whippets.
www.biorxiv.org/content/10.1...
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High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog’s genome
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
https://www.biorxiv.org/content/10.1101/2024.08.16.608262v1.abstract
about 1 year ago
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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.
over 1 year ago
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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....
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Your “out of the office” email is not fooling me | EMBO reports
EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.
https://www.embopress.org/doi/full/10.1038/s44319-024-00145-2
over 1 year ago
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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.
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Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
https://www.biorxiv.org/content/10.1101/2024.06.11.598575v1
over 1 year ago
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reposted by
J.J. Emerson 艾偉傑 🖥️🧬
Graham Coop
over 1 year ago
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...
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On forensic likelihood ratios from low-coverage sequencing
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
https://www.biorxiv.org/content/10.1101/2024.05.24.595821v1
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Adriana Briscoe elected to NAS.
news.uci.edu/2024/05/01/u...
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UC Irvine’s Adriana Briscoe is elected to the National Academy of Sciences
Renowned biologist is among 144 diverse recipients of prestigious award this year
https://news.uci.edu/2024/05/01/uc-irvines-adriana-briscoe-is-elected-to-the-national-academy-of-sciences/
over 1 year ago
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reposted by
J.J. Emerson 艾偉傑 🖥️🧬
Rich Meisel
over 1 year ago
📄 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-...
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Defensins of the Stable Fly (Stomoxys calcitrans) have Developmental-Specific Regulation and Evolve at Different Rates
Synopsis. Organisms produce antimicrobial peptides (AMPs) either in response to infection (induced) or continuously (constitutively) to combat microbes enc
https://academic.oup.com/icb/advance-article/doi/10.1093/icb/icae015/7651267?utm_source=authortollfreelink&utm_campaign=icb&utm_medium=email&guestAccessKey=c63dcde8-1cb8-403f-b271-ed2819a53b98
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Interesting. The original form of what became the "two button meme" was actually pretty good to begin with.
jake-clark.tumblr.com/post/1009467...
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jake-clark
<a href=
https://jake-clark.tumblr.com/post/100946716432
over 1 year ago
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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.
over 1 year ago
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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.
over 1 year ago
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Some artist played a lot of Mario Bros. games. That Tesla is Mario at 2:06.
www.youtube.com/watch?v=uylY...
add a skeleton here at some point
over 1 year ago
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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
over 1 year ago
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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!
over 1 year ago
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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!
over 1 year ago
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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...
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The world’s best subways: How these metro networks keep cities on the move | CNN
From Beijing to Budapest, these underground and overground metro networks move millions of people each day are some of the best metro lines on the planet.
https://www.cnn.com/travel/worlds-best-subways-metros/index.html
over 1 year ago
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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.
over 1 year ago
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Last ChatGPT anecdote of the day. It steers clear of taboo topics but apparently loves dad jokes.
over 1 year ago
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I've been chatting about D&D with an LLM.
over 1 year ago
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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.
over 1 year ago
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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.
over 1 year ago
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reposted by
J.J. Emerson 艾偉傑 🖥️🧬
bioRxiv Evolutionary Biology
over 1 year ago
Tree sequences as a general-purpose tool for population genetic inference https://www.biorxiv.org/content/10.1101/2024.02.20.581288v1
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Tree sequences as a general-purpose tool for population genetic inference https://www.biorxiv.org/content/10.1101/2024.02.20.581288v1
As population genetics data increases in size new methods have been developed to store genetic infor
https://www.biorxiv.org/content/10.1101/2024.02.20.581288v1
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Though long, I found this very interesting.
youtu.be/3Acx_n2WfYM?...
almost 2 years ago
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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.
almost 2 years ago
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I like to imagine grammar/spelling police happening upon Jeff's posts and feeling the self righteousness fade into confusion and finally petulant frustration.
add a skeleton here at some point
almost 2 years ago
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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.
almost 2 years ago
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reposted by
J.J. Emerson 艾偉傑 🖥️🧬
Chris Fiscus
almost 2 years ago
Attending
#PAG31
? Me too! Come see my talk about the evolution of grape crop wild relatives in the Grape Genome Initiative session on Sun!
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