J.J. Emerson 艾偉傑 🖥️🧬
@jjemerson.bsky.social
Evolutionary geneticist at UCI. JJ_Emerson on http://ecoevo.social.
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...
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
November 17, 2025 at 5:32 PM
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...
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
eppd13.cz?page_id=2587
The Specificity of the Hidden Defect in the Human Bio Element – EVROPSKÝ POLITICKÝ A PRÁVNÍ DISKURZ
eppd13.cz
November 6, 2025 at 9:46 PM
Here's a fun paper! The bibliography is fire. I wonder what they have to say about evolutionary genomics?
eppd13.cz?page_id=2587
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.
I'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
November 4, 2025 at 7:35 PM
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...
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
October 31, 2025 at 9:37 PM
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...
Reposted by J.J. Emerson 艾偉傑 🖥️🧬
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
October 31, 2024 at 6:06 PM
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.
October 27, 2025 at 7:41 PM
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.
Harvard 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
October 21, 2025 at 6:35 PM
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?
July 8, 2025 at 8:23 PM
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...
arstechnica.com/ai/2025/06/y...
June 11, 2025 at 9:28 PM
We were this close from Wikipedia hallucinations being fed into Google hallucinations.
arstechnica.com/ai/2025/06/y...
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.
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
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
Guest Post: Preprints Serve the Anti-science Agenda – This Is Why We Need Peer Review - The Scholarly Kitchen
Science is built on a foundation of rigor and credibility. Preprints are adding to the crumbling of that foundation, which is already under attack by anti-science political agendas.
scholarlykitchen.sspnet.org
April 22, 2025 at 7:45 PM
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...
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
March 13, 2025 at 7:21 PM
"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...
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?
February 3, 2025 at 5:09 PM
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.
January 24, 2025 at 11:42 PM
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.
Reposted by J.J. Emerson 艾偉傑 🖥️🧬
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
January 20, 2025 at 11:08 PM
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...
This is the foundational argument that eLife uses for its "publication" model. There are strident opponents to this idea.
January 15, 2025 at 2:00 AM
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.
In short, publish less, review more.
January 7, 2025 at 5:12 AM
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.
In short, publish less, review more.
Reposted by J.J. Emerson 艾偉傑 🖥️🧬
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
If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2
December 21, 2024 at 2:01 PM
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
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.
A 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.
December 21, 2024 at 1:40 AM
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!
December 20, 2024 at 11:05 PM
No more pencils, no more books, no more teacher's dirty looks!
Reposted by J.J. Emerson 艾偉傑 🖥️🧬
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 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
November 11, 2024 at 2:03 AM
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 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.
November 14, 2024 at 6:37 PM
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?
November 13, 2024 at 11:45 PM
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.
For me, it has to be setting up ssh keys with my servers.
November 8, 2024 at 6:53 PM
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.
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?
September 11, 2024 at 1:12 AM
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...
August 26, 2024 at 6:06 PM
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...