The centromere performs an essential function during cell division, yet its DNA sequence can evolve remarkably rapidly—a puzzle known as the centromere paradox. How can function remain conserved when sequence does not? 🧵 1/4
J.J. Emerson 艾偉傑 🖥️🧬
@jjemerson.bsky.social
Evolutionary geneticist at UCI. JJ_Emerson on http://ecoevo.social.
I know what I'm buying for Prime Day. I need some new reeds for my trombone. Ya gotta change those trombone reeds out frequently!
I’m always astounded when I remember that Gene Myers may be the most profound contributor among all bioinformaticians if you measure by how often his work is used by others. His diff algorithm is the basis for git diff. Just a weird little factoid that lives rent free in my brain.
❗🗳️ SMBE Election Reminder – check your inboxes! The SMBE election is currently underway through June 12, 2026. This is a friendly reminder to all SMBE members to check your spam inbox if you have not yet received your individual ballot. #society
It's so gratifying to see colleagues doing great things! Alex Samano and @mahulchak.bsky.social's latest paper is now in early access in Genome Research. It's a great read. Also, of the 13 authors, 11 are undergrads! genome.cshlp.org/content/earl...
Structural variants are enriched in deleterious visible phenotypes in Drosophila
Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation; yet, many evade discovery using short reads. While long-read sequencing can reveal hidden SVs, their role in organismal trait variation remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore Technologies long reads. These assemblies enable construction of a pangenome graph containing nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncover new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, the wing vein phenotype plexus (px1) links to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c1) wing phenotype links to a 7.5 kb DM412 retrotransposon disrupting the coding sequence of the muscle protein gene Strn-Mlck. We also identify a candidate intergenic enhancer for AblpeyD, a finding supported by CRISPR-Cas9. We also unveil 8 SV alleles of previously identified causal genes, including uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of genes causing phenotypic changes harbor candidate SVs >100 bp, whereas only 28% are expected based on euchromatic SVs. Together, our results indicate that SVs are strongly enriched among this class of large-effect, deleterious visible phenotypes in Drosophila.
genome.cshlp.org
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...
fastp: an ultra-fast all-in-one FASTQ preprocessor
AbstractMotivation. Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a differ
academic.oup.com
Here's a fun paper! The bibliography is fire. I wonder what they have to say about evolutionary genomics? eppd13.cz?page_id=2587
The Specificity of the Hidden Defect in the Human Bio Element – EVROPSKÝ POLITICKÝ A PRÁVNÍ DISKURZ
eppd13.cz
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.
Jeremy Yoder says no war@jbyoder.org · 9mo agoI'm not a Big Account by current Bluesky standards, I think, but I am mostly happy with the fuel mix of my Following feed and the kind of interaction I get, and I think it's mostly down to (1) I have replies set to followers-only by default, (2) I mute and block upon first offense, no discussion
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...
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
genome.cshlp.org
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...
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
github.com
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.
jon ben-menachem@jbenmenachem.com · 10mo agoHarvard is the 'best case scenario' for US research pedagogy (at least, financially). They have a $57bn endowment. I think the takeaway here is that the days of most PhD programs in the US are numbered
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.
David Green, PhD@ecologistgreen.bsky.social · last yr.Who’s with me? #PeerReview ensures the integrity of scientific knowledge. Science isn’t social media, and it’s dangerous to treat it as such. For this reason, I believe preprints serve an anti-science agenda & threaten our fields. Check out my editorial in @ScholarlyKitchen.bsky.social. 🧪 #SciPub
"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...
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
academic.oup.com
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
Kim Lab at UC Irvine
Visit the post for more.
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...
Shawn Burgess @burgesslab.bsky.social · 2y agoThis is the foundational argument that eLife uses for its "publication" model. There are strident opponents to this idea.
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.
Michael Eisen@mbeisen.bsky.social · 2y agoA truly bold public access policy would completely dissociate the NIH from the world of journals by refusing to pay into the corrupt and corrupting journal system, and directing NIH grantees to publish their work as preprints, exposing it to real and ongoing scrutiny.
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.
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.
github.com
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...