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Pavel Dimens

@pvdimens.bsky.social
169 followers 154 following 95 posts

A PhD in population genetics of marine fishes, Julia package dev, linked-read aficionado, guitar player, rock climber, and once described as endearingly mediocre.

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Pavel Dimens @pvdimens.bsky.social · 4h
I wish LinkedIn had a prompt after someone tries to post something. It would be a likert scale asking you to self assess how much value do you really think the post has. And yes I recognize the hypocrisy of whining about that here 😅
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Maria Akopyan, PhD @akopyan.bsky.social · 10/09/2026
📣 I'm recruiting PhD students to join the Akopyan Lab at Rice University! If you're passionate about evolutionary genomics, I'd love to hear from you. Details: akopyanlab.org/opportunities Please share widely! 🙏
akopyanlab.org
Opportunities
We are recruiting PhD students in Evolutionary Genomics for Fall 2027 at Rice University!  Projects in the lab include investigating the causes and consequences of recombination rate variation, the...
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Pavel Dimens @pvdimens.bsky.social · 14/09/2026
Yes, Gemini, I developed Harpy under the pseudonym Peter Dimens � #AI #bioinformatics
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Pavel Dimens @pvdimens.bsky.social · 06/09/2026
I host a bad movie night on the last weekend of every month. I think I nailed this month's poster.
A very poorly hand drawn sign reading bad movie night and details about it, with a very simple bull-like creature depicted on it to represent the main character from the movie Niu Lai
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Carl Zimmer @carlzimmer.com · 01/09/2026
UNC-Chapel Hill, Duke to combine herbaria, creating the third-largest university plant collection in the United States ncbg.unc.edu/2026/08/31/u...
ncbg.unc.edu
UNC-Chapel Hill, Duke to combine herbaria, creating the third-largest university plant collection in the United States - North Carolina Botanical Garden
The combined herbaria will create an unmatched archive for studying plant diversity in the southeastern United States (Chapel Hill, N.C.— Aug. 31, 2026) UNC-Chapel Hill and Duke University will unite....
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Julie Cruse @academicabuse.com · 23/08/2026
Tired of being stuffed into the #IvoryCloset by university bad actors and coverups? Come find a way out: buff.ly/wuDf8vr #RecoveringAcademic 🪜 🎓 📜 🍎 ♀️ #PhDSky #Blackademia #AcademicChatter #AcademicSky #MeToo #HigherEd #PhDChat #WomenInStem
buff.ly
Academic Recovery Workbook | Academic Abuse
Academia shapes you slowly and without asking permission. This free reflection tool helps you see how and find your way back to who you were before it did.
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Azwad Iqbal @azwadiqbal.bsky.social · 08/08/2026
BLink-seq is out! Linked-read sequencing that brings phased whole-genome data to non-model species at population scale. We show it phases haplotypes and detects SVs, revealing previously undocumented structural complexity in an adaptive Atlantic silverside inversion. www.biorxiv.org/content/10.6...
biorxiv.org
BLink-seq delivers population-scale haplotypes without long reads: a scalable framework for non-model genomics
Information about segregating haplotypes and structural variation (SV) can be extremely rich for a variety of applications in population genomics but remains largely inaccessible for many non-model sp...
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Pavel Dimens @pvdimens.bsky.social · 08/08/2026
So happy to announce our preprint for BLink-seq linked-read sequencing is live! Tremendous work by Azwad, Jen, and Nina! We also launched a website that is slowly becoming the repository of general linked-read knowledge 🙂https://doi.org/10.64898/2026.08.03.742036 blinkseq.github.io
blinkseq.github.io
Bead-Barcoded Linked-read Sequencing
Linking sequences and beyond
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Leonie Moyle @speciationlab.bsky.social · 06/08/2026
Interested in genetics, diversification, and speciation? We're hiring a Research Associate to help with our projects, including the convergent evolution of fruit color. Come and work with us! Feel free to contact me with questions. (Reposts appreciated!) Link: indiana.peopleadmin.com/postings/33973
a matrix of 6 different Solanum (wild tomato) species with six different fruit colors, ranging from white to bright red.
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Pavel Dimens @pvdimens.bsky.social · 06/08/2026
actual text message I sent today: "Borscht with 3 Cs" I assume this is why anyone follows this account?
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Pavel Dimens @pvdimens.bsky.social · 01/08/2026
Today begins the 30day clock until my funding runs out. I've been frantically applying to all sorts of jobs (all rejections 🫩). So if anyone here knows of someone hiring a molecular ecologist real good at field work and bioinformatics, please do let me know 🙏
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Dr David S Anderson @dsaarchaeology.bsky.social · 10/07/2026
Original Tweet from @Mantia: What’s something that seems obvious within your profession, but the general public seems to misunderstand?

Quote tweet from @hwitteman: That $35 that scientific journals charge you to read a paper goes 100% to the publisher, 0% to the authors. If you just email us to ask for our papers, we are allowed to send them to you for free, and we will be genuinely delighted to do so.
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Quy Ma @quyma.bsky.social · 02/07/2026
97% of human history ran on legal slavery. We’ve had 3% without it, and even that’s generous: ~28 million people are in forced labor globally right now. It never actually ended. It just kept changing its name. My latest essay on Substack. #econsky #polisky #history #academicsky
open.substack.com
The Slave Economy Never Ended. It Just Changed Its Labor Source.
What Rome's slave economy tells us about who should own the one we're building now, and the only version worth building.
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 19/06/2026
We are excited to announce that the 2026 Great Lakes Annual Meeting of Evolutionary Genomics (GLAM-EvoGen) will take place on Saturday, August 15, 2026 at the University at Buffalo. More information is available on our website: gokcumenlab.org/glam2026/ @gokcumenlab.bsky.social
gokcumenlab.org
GLAM2026 – Gokcumen Lab
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Pavel Dimens @pvdimens.bsky.social · 27/06/2026
10 on-and-off months of learning #Golang later, I seem to have gotten my fork of the Lariat linked-read aligner, Arachne, working. If you got modern linked read data, I'd love for you to try it out and report back! #bioinformatics pdimens.github.io/arachne
pdimens.github.io
Arachne linked-read aligner | Arachne
Arachne is a fork intended to be a revival and [hopefully] continuation of Lariat, the linked-read aware aligner created by 10X Genomics and bundled in their LongRanger pipeline.
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Pavel Dimens @pvdimens.bsky.social · 16/04/2026
Well, AI slop finally became personal. A (presumably) well-meaning person outside of biology decided to reimplement all of the highly optimized and specialized packages in BioJulia into a single package using AI.
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Pavel Dimens @pvdimens.bsky.social · 03/11/2025
A be-floor and after of what I've been doing when I come home from work
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Thibault (Tibo) Leroy @tiboleroyinen.bsky.social · 18/09/2025
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
tiris.univ-toulouse.fr
AToUT – TIRIS – Toulouse's Science In and For Society
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Mike Moore @moore-evo-eco.bsky.social · 18/08/2025
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...
docs.google.com
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...
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WIRED @wired.com · 23/09/2025
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."
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Pavel Dimens @pvdimens.bsky.social · 24/09/2025
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...
github.com
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
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Pavel Dimens @pvdimens.bsky.social · 05/09/2025
Band Name Idea; Blood Bath & Beyond Debut Album: Bath Salts
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Julie Cruse @academicabuse.com · 01/09/2025
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
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Pavel Dimens @pvdimens.bsky.social · 01/09/2025
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.
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Pavel Dimens @pvdimens.bsky.social · 28/08/2025
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
The software logo, text that reads "Harpy" and a badge beside the text that indicates it's version 3.0
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Sam Yeaman @samyeaman.bsky.social · 20/08/2025
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/...
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Pavel Dimens @pvdimens.bsky.social · 20/08/2025
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...
A logo featuring the word "Arachne", where the "h" is depicted as a half-spider humanoid knitting what looks like DNA
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Pavel Dimens @pvdimens.bsky.social · 16/08/2025
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?
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Pavel Dimens @pvdimens.bsky.social · 15/08/2025
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
Quit Yer Mouthbreathing–The open cup – Apple Podcasts
Podcast Episode · The open cup · 15/08/2025 · 21m
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Pavel Dimens @pvdimens.bsky.social · 14/08/2025
This morning, my sister told me that they're making The Mask 3 and I've been stressed ever since.
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Pavel Dimens @pvdimens.bsky.social · 08/08/2025
In the year of our lord 2025, I don't see why `scale_color_brewer()` is still case sensitive for the color palette
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Pavel Dimens @pvdimens.bsky.social · 04/08/2025
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.
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Pavel Dimens @pvdimens.bsky.social · 02/08/2025
"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 🐉
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Pavel Dimens @pvdimens.bsky.social · 21/07/2025
The Mimick logo has been updated to reflect its new #julialang codebase 👀🙌
A minimal cartoon of a treasure chest with teeth, featuring three circles in a triangle as an "eye"
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Pavel Dimens @pvdimens.bsky.social · 17/07/2025
If you've ever wondered how the sausage gets made over here in Harpy land, behold
A series of failed continuous integration tests trying to introduce a new feature. The topmost test, titled "I guess we can't have nice things" is the only one that succeeded.
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Pavel Dimens @pvdimens.bsky.social · 17/07/2025
Been writing in #Julialang again and BOY does it feel good. 😌
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Pavel Dimens @pvdimens.bsky.social · 06/07/2025
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 🎸
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Pavel Dimens @pvdimens.bsky.social · 23/06/2025
Mimick now works with circular DNA, far all you microbial linked-read enthusiasts 🦠🧬 Go out and simulate you some data 💪 github.com/pdimens/mimick
github.com
GitHub - pdimens/mimick: Linked-read sequence simulator
Linked-read sequence simulator. Contribute to pdimens/mimick development by creating an account on GitHub.
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Pavel Dimens @pvdimens.bsky.social · 19/06/2025
According to Facebook, 8yrs ago today was the greatest day of my life
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Pavel Dimens @pvdimens.bsky.social · 18/06/2025
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) 😁
bsky.app
@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
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Pavel Dimens @pvdimens.bsky.social · 14/06/2025
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.
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Julia Van Etten @couchmicroscopy.bsky.social · 11/06/2025
Never in a million years did I think I’d be having regular conversations with my peers (most of them are other PRFB postdocs) about what we plan to do with our lives if we can’t be scientists anymore, i.e., if all the jobs continue disappearing. It’s all very bleak as an ECR right now.
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-𝚖𝚘𝚡 @moxiest.art · 11/06/2025
leftists: that thing you teach us in school to be terrified of is happening historians: that thing is definitely happening star wars: here is a beat-for-beat breakdown of how the thing happens, but with pew pew lasers. we know you watched it news outlets: these protesters are out of control
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Pavel Dimens @pvdimens.bsky.social · 09/06/2025
7 months ago, in a mtg with Nina, she said I should absolutely not write a linked read simulator. And I didn't, I improved on an existing one. But then it became mine. And then I rewrote the entire thing 👀. So anyway, Mimick v2 is out. Simulate some linked reads, y'all. github.com/pdimens/mimick
github.com
GitHub - pdimens/mimick: Linked-read sequence simulator
Linked-read sequence simulator. Contribute to pdimens/mimick development by creating an account on GitHub.
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Pavel Dimens @pvdimens.bsky.social · 12/05/2025
Has anyone here been an editor for a sci journal and has wisdom to share about their experience?
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Pavel Dimens @pvdimens.bsky.social · 07/05/2025
Landlocked? Yes. Undeterred? Also yes.
Text on a printed page that reads it's the first annual Cornell Oceans Symposium
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Pierre de Villemereuil @pdevillemereuil.bsky.social · 05/05/2025
There is still a few days to apply to this PhD offer! Come enjoy Paris and the "Jardin des Plantes" at the heart of it, while working on exciting science!
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Pavel Dimens @pvdimens.bsky.social · 05/05/2025
In Jan bought my first house and have been gradually learning about all the insane choices the previous owners made. Today, I learned that one of the floors is laminate over FOUR previous linoleum floors. Four. Which means it's a total of 5 floors. The top 2 lino floors were... THE SAME LINOLEUM 😶
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Chloé Schmidt @chloology.bsky.social · 21/04/2025
I’m recruiting a PhD student in macrogenetics at Dalhousie University 🇨🇦! Focus will be on the biogeography of vertebrate genetic diversity or urban evolutionary ecology. Full ad: www.schmidt-biodiversity-lab.org/macrogenetic... If the ad is up, applications are still open. Please share widely! 🧬🧬
schmidt-biodiversity-lab.org
Macrogenetics PhD position | schmidt-biodiversity-lab
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Sabhrina Aninta @sagitaninta.bsky.social · 29/04/2025
Anyone knows any QC pipeline for PacBio data as well as pipeline for de novo assembly? #consgen #popgen
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