Pavel Dimens
@pvdimens.bsky.social
A PhD in population genetics of marine fishes, Julia package dev, linked-read aficionado, guitar player, rock climber, and once described as endearingly mediocre.
Pinned
Pavel Dimens
@pvdimens.bsky.social
· Mar 28
Not-so-gentle reminder that GCRL at the U. of Southern Mississippi has some truly reprehensible PI's who you should be wary of and they keep being elevated into positions of power.
A be-floor and after of what I've been doing when I come home from work
November 3, 2025 at 10:09 PM
A be-floor and after of what I've been doing when I come home from work
Reposted by Pavel Dimens
Fifteen 2-year postdoc fellowships available at U. Toulouse 😍 through a MSCA-COFUND (AToUT tiris.univ-toulouse.fr/en/programs/...)
Interested to apply for a postdoctoral research project focusing on the genomics of farm animals or pollinators? Let me know!
Eligibility: <1 yr in 🇫🇷 in the last 3 yrs
Interested to apply for a postdoctoral research project focusing on the genomics of farm animals or pollinators? Let me know!
Eligibility: <1 yr in 🇫🇷 in the last 3 yrs
AToUT – TIRIS – Toulouse's Science In and For Society
tiris.univ-toulouse.fr
September 18, 2025 at 6:33 PM
Fifteen 2-year postdoc fellowships available at U. Toulouse 😍 through a MSCA-COFUND (AToUT tiris.univ-toulouse.fr/en/programs/...)
Interested to apply for a postdoctoral research project focusing on the genomics of farm animals or pollinators? Let me know!
Eligibility: <1 yr in 🇫🇷 in the last 3 yrs
Interested to apply for a postdoctoral research project focusing on the genomics of farm animals or pollinators? Let me know!
Eligibility: <1 yr in 🇫🇷 in the last 3 yrs
Reposted by Pavel Dimens
Are you looking for a PhD position and want to spend your summers in the Rocky Mountains?
My lab @cudenverclas.bsky.social is looking for 1 PhD student to work on a NSF-funded project to study elevational range shifts in Colorado! 🧪🌍🐙
Apply by Nov 1!
Details here docs.google.com/document/d/1...
My lab @cudenverclas.bsky.social is looking for 1 PhD student to work on a NSF-funded project to study elevational range shifts in Colorado! 🧪🌍🐙
Apply by Nov 1!
Details here docs.google.com/document/d/1...
2025 - Hypoxia PhD job ad
The Moore lab at the University of Colorado Denver is searching for 1 Ph.D. student to study the elevational limits of dragonflies in Colorado (http://moore-evo-eco.weebly.com). This position is fully...
docs.google.com
August 18, 2025 at 1:02 PM
Are you looking for a PhD position and want to spend your summers in the Rocky Mountains?
My lab @cudenverclas.bsky.social is looking for 1 PhD student to work on a NSF-funded project to study elevational range shifts in Colorado! 🧪🌍🐙
Apply by Nov 1!
Details here docs.google.com/document/d/1...
My lab @cudenverclas.bsky.social is looking for 1 PhD student to work on a NSF-funded project to study elevational range shifts in Colorado! 🧪🌍🐙
Apply by Nov 1!
Details here docs.google.com/document/d/1...
Reposted by Pavel Dimens
A 12-foot statue of Donald Trump and Jeffrey Epstein frolicking and holding hands appeared on the National Mall in Washington, DC on Tuesday, September 23.
A plaque under the statue states that it has been erected “In Honor of Friendship Month."
A plaque under the statue states that it has been erected “In Honor of Friendship Month."
September 23, 2025 at 10:44 PM
A 12-foot statue of Donald Trump and Jeffrey Epstein frolicking and holding hands appeared on the National Mall in Washington, DC on Tuesday, September 23.
A plaque under the statue states that it has been erected “In Honor of Friendship Month."
A plaque under the statue states that it has been erected “In Honor of Friendship Month."
I didn't love how monolithic Harpy was becoming with novel features. So, the file-modification things were split out into Djinn. So, use Djinn if you need to convert linked-read fastq/bams
#bioinformatics
github.com/pdimens/djin...
#bioinformatics
github.com/pdimens/djin...
GitHub - pdimens/djinn: Convert linked-read FASTQ/BAM files between formats, like magic.
Convert linked-read FASTQ/BAM files between formats, like magic. - pdimens/djinn
github.com
September 24, 2025 at 1:11 AM
I didn't love how monolithic Harpy was becoming with novel features. So, the file-modification things were split out into Djinn. So, use Djinn if you need to convert linked-read fastq/bams
#bioinformatics
github.com/pdimens/djin...
#bioinformatics
github.com/pdimens/djin...
Band Name Idea;
Blood Bath & Beyond
Debut Album:
Bath Salts
Blood Bath & Beyond
Debut Album:
Bath Salts
September 5, 2025 at 11:48 AM
Band Name Idea;
Blood Bath & Beyond
Debut Album:
Bath Salts
Blood Bath & Beyond
Debut Album:
Bath Salts
Reposted by Pavel Dimens
Hi, I’m Julie Cruse. I created AcademicAbuse.com – a dashboard of data, resources & tools to help survivors of academic abuse survive and safely speak out. (1/9 🧵)
🪜 🎓 📜 🍎 ♀️ 👩🏾🔬 👩🏼🔬 👩🏾🎓 #PhDSky #Blackademia #AcademicChatter #AcademicSky #MeToo #HigherEd #PhDChat #TimesUpHigherEd
🪜 🎓 📜 🍎 ♀️ 👩🏾🔬 👩🏼🔬 👩🏾🎓 #PhDSky #Blackademia #AcademicChatter #AcademicSky #MeToo #HigherEd #PhDChat #TimesUpHigherEd
September 1, 2025 at 1:20 AM
Hi, I’m Julie Cruse. I created AcademicAbuse.com – a dashboard of data, resources & tools to help survivors of academic abuse survive and safely speak out. (1/9 🧵)
🪜 🎓 📜 🍎 ♀️ 👩🏾🔬 👩🏼🔬 👩🏾🎓 #PhDSky #Blackademia #AcademicChatter #AcademicSky #MeToo #HigherEd #PhDChat #TimesUpHigherEd
🪜 🎓 📜 🍎 ♀️ 👩🏾🔬 👩🏼🔬 👩🏾🎓 #PhDSky #Blackademia #AcademicChatter #AcademicSky #MeToo #HigherEd #PhDChat #TimesUpHigherEd
Since finishing my PhD in 2022 I have:
1. Rediscovered my belly laugh
2. Cried at my first wedding
Hard to describe how powerful it is to acknowledge healing.
1. Rediscovered my belly laugh
2. Cried at my first wedding
Hard to describe how powerful it is to acknowledge healing.
September 1, 2025 at 2:14 AM
Since finishing my PhD in 2022 I have:
1. Rediscovered my belly laugh
2. Cried at my first wedding
Hard to describe how powerful it is to acknowledge healing.
1. Rediscovered my belly laugh
2. Cried at my first wedding
Hard to describe how powerful it is to acknowledge healing.
My lil' baby turns 3.0 today! Most notable features:
- autodetection of linked-read types (and not linked-read WGS too!)
- more debuggin' and troubleshootin' options
#bioinformatics #genomics #linkedreads
- autodetection of linked-read types (and not linked-read WGS too!)
- more debuggin' and troubleshootin' options
#bioinformatics #genomics #linkedreads
August 28, 2025 at 7:14 PM
My lil' baby turns 3.0 today! Most notable features:
- autodetection of linked-read types (and not linked-read WGS too!)
- more debuggin' and troubleshootin' options
#bioinformatics #genomics #linkedreads
- autodetection of linked-read types (and not linked-read WGS too!)
- more debuggin' and troubleshootin' options
#bioinformatics #genomics #linkedreads
Reposted by Pavel Dimens
I'm looking to recruit a PhD student to study patterns of local adaptation and introgression across the spruce hybrid zone in the Rockies near Calgary. Projects can include field work, bioinformatics, pop gen theory, or comparison to plant/ conifer species
yeamanlab.weebly.com/uploads/5/7/...
yeamanlab.weebly.com/uploads/5/7/...
August 20, 2025 at 8:19 PM
I'm looking to recruit a PhD student to study patterns of local adaptation and introgression across the spruce hybrid zone in the Rockies near Calgary. Projects can include field work, bioinformatics, pop gen theory, or comparison to plant/ conifer species
yeamanlab.weebly.com/uploads/5/7/...
yeamanlab.weebly.com/uploads/5/7/...
Today, that Go project *finally compiled*! It only took 7 complete project restructuring attempts. Now that it builds, the real work begins, and it's a good time to reveal I'm trying to revive Lariat, the linked-read aligner written by 10X Genomics. It's called Arachne 😁🕷️ github.com/pdimens/arac...
August 20, 2025 at 6:53 PM
Today, that Go project *finally compiled*! It only took 7 complete project restructuring attempts. Now that it builds, the real work begins, and it's a good time to reveal I'm trying to revive Lariat, the linked-read aligner written by 10X Genomics. It's called Arachne 😁🕷️ github.com/pdimens/arac...
I'm trying to revive an abandoned #bioinformatics software written Go. I have no experience with Go (or similar langs), but doing my best. Does anyone here have even middling experience with Go that can lend some wisdom or time towards this effort?
August 16, 2025 at 12:26 PM
I'm trying to revive an abandoned #bioinformatics software written Go. I have no experience with Go (or similar langs), but doing my best. Does anyone here have even middling experience with Go that can lend some wisdom or time towards this effort?
There's a coffee tasting podcast and ya boi has a guest spot on it this week cupping Don't Be Alarmed by Coffeemania. Y'all should give their stuff a listen ☕
podcasts.apple.com/gb/podcast/q...
podcasts.apple.com/gb/podcast/q...
Quit Yer Mouthbreathing–The open cup – Apple Podcasts
Podcast Episode · The open cup · 15/08/2025 · 21m
podcasts.apple.com
August 15, 2025 at 10:37 AM
There's a coffee tasting podcast and ya boi has a guest spot on it this week cupping Don't Be Alarmed by Coffeemania. Y'all should give their stuff a listen ☕
podcasts.apple.com/gb/podcast/q...
podcasts.apple.com/gb/podcast/q...
This morning, my sister told me that they're making The Mask 3 and I've been stressed ever since.
August 14, 2025 at 10:38 PM
This morning, my sister told me that they're making The Mask 3 and I've been stressed ever since.
In the year of our lord 2025, I don't see why `scale_color_brewer()` is still case sensitive for the color palette
August 8, 2025 at 11:40 AM
In the year of our lord 2025, I don't see why `scale_color_brewer()` is still case sensitive for the color palette
Out of necessity, I've recently got into reviving abandoned/dead linked-read bioinformatics software. Can be seen as software necromancy or adoption, depending on what you consider abandonware. I prefer calling it necromancy, tbh.
August 4, 2025 at 6:50 PM
Out of necessity, I've recently got into reviving abandoned/dead linked-read bioinformatics software. Can be seen as software necromancy or adoption, depending on what you consider abandonware. I prefer calling it necromancy, tbh.
"How hard can it be?" he thought to himself before taking on another time-sucking project he is grossly unqualified to have even considered.
Anyway, if this works, expect another linked read software with another monster/creature name 🐉
Anyway, if this works, expect another linked read software with another monster/creature name 🐉
August 2, 2025 at 2:46 AM
"How hard can it be?" he thought to himself before taking on another time-sucking project he is grossly unqualified to have even considered.
Anyway, if this works, expect another linked read software with another monster/creature name 🐉
Anyway, if this works, expect another linked read software with another monster/creature name 🐉
The Mimick logo has been updated to reflect its new #julialang codebase 👀🙌
July 21, 2025 at 2:23 PM
The Mimick logo has been updated to reflect its new #julialang codebase 👀🙌
If you've ever wondered how the sausage gets made over here in Harpy land, behold
July 17, 2025 at 8:45 PM
If you've ever wondered how the sausage gets made over here in Harpy land, behold
Been writing in #Julialang again and BOY does it feel good. 😌
July 17, 2025 at 11:29 AM
Been writing in #Julialang again and BOY does it feel good. 😌
The world is crazy, still. Writing anything at all on social media feels stupid. But, I started learning to play Jake E. Lee's solo from Bark at the Moon and I guess I'm writing it here to 1. still somehow interact with the world and 2. foolishly hold myself accountable 🎸
July 6, 2025 at 4:46 AM
The world is crazy, still. Writing anything at all on social media feels stupid. But, I started learning to play Jake E. Lee's solo from Bark at the Moon and I guess I'm writing it here to 1. still somehow interact with the world and 2. foolishly hold myself accountable 🎸
Mimick now works with circular DNA, far all you microbial linked-read enthusiasts 🦠🧬
Go out and simulate you some data 💪
github.com/pdimens/mimick
Go out and simulate you some data 💪
github.com/pdimens/mimick
GitHub - pdimens/mimick: Linked-read sequence simulator
Linked-read sequence simulator. Contribute to pdimens/mimick development by creating an account on GitHub.
github.com
June 23, 2025 at 1:51 PM
Mimick now works with circular DNA, far all you microbial linked-read enthusiasts 🦠🧬
Go out and simulate you some data 💪
github.com/pdimens/mimick
Go out and simulate you some data 💪
github.com/pdimens/mimick
According to Facebook, 8yrs ago today was the greatest day of my life
June 19, 2025 at 2:12 PM
According to Facebook, 8yrs ago today was the greatest day of my life
Oh hey, the Harpy paper is out. The software's been available, but it's nice to have something in writing! It also works with other linked read data and non-linked data (wgs, rad) 😁
@bioinfoadv.bsky.social on Bluesky
🧬 Explore the latest from Bioinformatics Advances: “Harpy: A pipeline for processing haplotagging linked-read data”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf133
Authors include: @pvdimens.bsky.social
bsky.app
June 18, 2025 at 11:29 AM
Oh hey, the Harpy paper is out. The software's been available, but it's nice to have something in writing! It also works with other linked read data and non-linked data (wgs, rad) 😁
Today was a really frustrating analytical/bioinformatics day and the entire time I had JLos catalog blasting in my headphones and it's 2am and I'm still reconciling the conflicting emotions about all of that.
June 14, 2025 at 6:29 AM
Today was a really frustrating analytical/bioinformatics day and the entire time I had JLos catalog blasting in my headphones and it's 2am and I'm still reconciling the conflicting emotions about all of that.