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Lucas van Dijk

@lucasvandijk.nl
205 followers 386 following 67 posts

Bioinformatics Software Engineer @ @pacbio.bsky.social 🧬🖥️. Previously at the data sciences platform and bacterial genomics group @ @broadinstitute.org. Interested in algorithm development, human genetics, and the microbiome.

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Lucas van Dijk @lucasvandijk.nl · 29/08/2026
This is awesome news!
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Lucas van Dijk @lucasvandijk.nl · 23/07/2026
What a huge achievement! 450 human haplotypes. PacBio Kinnex transcriptomic data, Fiber-Seq (nucleosome occupancy), and so much more!
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Lucas van Dijk @lucasvandijk.nl · 11/06/2026
It’s really ridiculous how quickly it flags anything biology or bioinformatics
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PacBio @pacbio.bsky.social · 26/05/2026
SPRQ-Nx chemistry is now shipping worldwide, bringing sub-$300 HiFi genomes to the Revio platform! This global rollout cuts sequencing costs by 30%, making it easier than ever to scale high-throughput workflows Full press release here: bit.ly/49HwmcL #SPRQNx #PacBio #HiFisequencing #Revio
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Alex Crits-Christoph @acritschristoph.bsky.social · 27/04/2026
oh that's very very cool:
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Lucas van Dijk @lucasvandijk.nl · 13/04/2026
Mood
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Lucas van Dijk @lucasvandijk.nl · 18/03/2026
HiFi sequencing of many, many metagenomes!
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 11/03/2026
So what's the most interesting, or weirdest, application of hidden markov models (HMMs) that you've seen? I once built an HMM for sage grouse mating behavior, fit to data collected by a robotic grouse (pictured doi.org/10.1086/703518). Looking for other examples for a new lecture on HMMs.
The robotic female sage-grouse, shown here, was used to experimentally manipulate sage-grouse males’ courtship behavior via remote control.
[Photo credit: Anna C. Perry]
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Lucas van Dijk @lucasvandijk.nl · 30/11/2025
That x86 ABI mug is going to be powering my mornings :)
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Lucas van Dijk @lucasvandijk.nl · 28/11/2025
I am very excited to have started a new role as a senior software engineer at @pacbio.bsky.social! I’ll be joining the instrument analysis team developing high-performance software on instrument delivering those beautiful HiFi reads to you 😁
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Mike Schatz @mikeschatz.bsky.social · 14/10/2025
Getting excited for #ASHG25. The must see talk is tomorrow at 1:30 by Qiuhui (Iris) Li presenting the first large-scale integration of long-read genome sequencing with electronic health record data across >1000 All of Us participants meetings.ashg.org/event/ASHG25...
meetings.ashg.org
PheedLoop
PheedLoop: Hybrid, In-Person & Virtual Event Software
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Lucas van Dijk @lucasvandijk.nl · 07/10/2025
>1,000 human genomes sequenced with PacBio HiFi, offering many new insights into human structural variation and its associations with disease. www.medrxiv.org/content/10.1...
medrxiv.org
Population-scale Long-read Sequencing in the All of Us Research Program
The All of Us Research Program (AoU) is a national biobank seeking to enroll one million individuals in the United States to link genomic and biomedical data, including short- and long-read whole-geno...
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Erik Garrison @thinks.lol · 17/07/2025
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
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Alexandria Ocasio-Cortez @aoc.bsky.social · 03/07/2025
I am grieving the barbarism that is going to unfurl from all this. People are going to die. Livelihoods gone. All to feed a corrupt kleptocracy. I see every day up close how different it is from the first time around. There are no guardrails. A disaster. I’m sorry we have to live through this.
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Lucas van Dijk @lucasvandijk.nl · 17/02/2025
The efficiency of the market
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Lucas van Dijk @lucasvandijk.nl · 17/02/2025
What the actual fuck is this
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Lucas van Dijk @lucasvandijk.nl · 11/02/2025
And now officially out in Oxford Bioinformatics :) academic.oup.com/bioinformati...
academic.oup.com
Fast and exact gap-affine partial order alignment with POASTA
AbstractMotivation. Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pa
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Lucas van Dijk @lucasvandijk.nl · 09/02/2025
For those using WDL for their bioinformatic workflows: I wrote an extension for the @zed.dev code editor enabling syntax highlighting and integration with wdl-lsp. It also supports bash highlighting in command blocks. Installable through the Zed extensions pane! github.com/broadinstitu...
Screenshot of the Zed editor showcasing syntax highlighting for the Workflow Description Language.
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Lucas van Dijk @lucasvandijk.nl · 27/01/2025
A printed thesis! Did not expect it would feel so good to have the final version physically in your hands 🙌
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Nature Reviews Genetics @natrevgenet.nature.com · 27/01/2025
Diversity and consequences of structural variation in the human genome go.nature.com/4awEtaY #Review by Ryan L. Collins & Michael E. Talkowski @broadinstitute.org @harvard.edu @harvardmed.bsky.social
go.nature.com
Diversity and consequences of structural variation in the human genome - Nature Reviews Genetics
Collins and Talkowski provide a broad overview of structural variation in the human genome that covers their mutational properties, the dynamics of population genetics and functional consequences in d...
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qntm @qntm.org · 17/01/2025
COMPUTER SCIENTISTS: "k" means one thousand and twenty-four STORAGE MANUFACTURERS: "k" means one thousand DISPLAY MANUFACTURERS [thinking hard]: "K" means nine hundred and sixty
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Travis Wheeler @wheelerlab.org · 07/01/2025
Still in beta, so possible minor API changes ... but our Suffix Array library (in Rust) is ready for business. Builds on lovely ideas in CaPS-SA from @robp.bsky.social. Low mem construction. Spaced seeds. Optional crazy-low-mem search. More info on the horizon.
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Ming Tommy Tang @tommytang.bsky.social · 07/01/2025
5/ In my experience, most of the time, you don’t need deep learning. Often, simple methods like linear regression or random forests work well — especially for moderate-sized datasets. Deep learning excels in image analysis & protein structure prediction.
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Lucas van Dijk @lucasvandijk.nl · 25/11/2024
Anyone insight how I can configure pylsp such that it finds and autocompletes packages installed with uv?
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Lucas van Dijk @lucasvandijk.nl · 19/11/2024
Found ChatGPT in Fallout New Vegas: "Are you some kind of AI?" "Regrettably not, sir. All modules in this habitat are synthetic personalities atop a mundane operating system. There is no intelligence here, sir." www.youtube.com/watch?v=4XJw...
A view of the Central Intelligence Unit in Fallout New Vegas: Old World Blues.
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Bluesky @bsky.app · 15/11/2024
💡 Tip: You can set your website as your username on Bluesky! This is one form of self-verification, and we especially encourage official organizations and brands to do this! Examples include @npr.org @react.dev @duolingobrasil.com.br. Here's our guide for how to do this:
bsky.social
How to set your domain as your handle - Bluesky
Using a domain as your handle helps with account identity, verification, and portability. Here's how to set your domain as your handle.
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Lucas van Dijk @lucasvandijk.nl · 14/11/2024
I want to hear some bioinformatics war stories! What was the most weird bug or sequencing artifact you had to debug? I'll start: Did you know that changing the number of threads used by bwa-mem can influence your BAM output?
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Thibaut Brunet @thibautbrunet.bsky.social · 11/11/2024
[looking at Bluesky over the past 2 days] So this is what the Cambrian explosion must have felt like
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Lucas van Dijk @lucasvandijk.nl · 12/11/2024
I think Philip Eng deserves a statue in the Boston common
MBTA subway map showing only a handful of remaining slow zones
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Lucas van Dijk @lucasvandijk.nl · 26/10/2024
Working through Prince's excellent "Understanding Deep Learning" book. Full of great insights like these: by optimizing using SGD we implicitly regularize the weights towards values where the gradients are similar across batches 🤯
The equation shows the updated loss function for SGD with the regularization term.
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 10/10/2024
The protein emoji was rejected in 2022. With the #alphafold #proteindesign #chemnobel, it's the perfect time for a revival ! go go @lindorfflarsen.bsky.social and col. !!!!!
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Bryce Covert @brycecovert.bsky.social · 19/06/2024
Photo of a fake MTA sign saying the G will not be getting signal upgrades because Gov. Kathy Hochul canceled congestion pricing.
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Lucas van Dijk @lucasvandijk.nl · 28/05/2024
Excited to share a new preprint! We developed a new algorithm for POA, POASTA (pronounce it with your best Bo-ah-ston accent). It is based on the A* framework and inspired by other recent alignment algorithms such as the WFA and Astarix. www.biorxiv.org/content/10.1...
biorxiv.org
Fast and exact gap-affine partial order alignment with POASTA
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Jay Rosen @jayrosen.bsky.social · 08/05/2024
"To Kahn, democracy is a partisan issue and he’s not taking sides." Think about that for a moment. Dan Froomkin says the old guard at the New York Times has reasserted control "over the rabble," and Joe Kahn's interview with Ben Smith demonstrates it. presswatchers.org/2024/05/new-...
presswatchers.org
New York Times editor Joe Kahn says defending democracy is a partisan act and he won’t do it | Press Watch
Joe Kahn, after two years in charge of the New York Times newsroom, has learned nothing.
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StreetsblogMASS @mass.streetsblog.org · 23/04/2024
Advocates Win Concessions As State Starts Value-Engineering Allston I-90 Megaproject
dlvr.it
Advocates Win Concessions As State Starts Value-Engineering Allston I-90 Megaproject
In the past month, MassDOT has agreed to two significant changes in its Allston I-90 megaproject in response to pressures from sustainable transportation advocates. Although MassDOT won a $335 million federal grant to help pay for the project earlier this…
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Hayes Brown @hayesbrown.bsky.social · 05/04/2024
an earthquake three days before a total eclipse of the sun would absolutely have taken out a whole ass dynasty back in the day
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 13/03/2024
(Did I never post this tip here?) Do you like bibtex? Do you do doi? Do you want bibtex refs from doi on the command line? Yes you do, you wonderful monster. Try this line (adjust doi as needed, and see alt text for source too): curl -LH "Accept: application/x-bibtex" doi.org/10.1002/evan...
Shell output:

curl -LH "Accept: application/x-bibtex" https://doi.org/10.1002/evan.10110

 @article{Henrich_2003, title={The evolution of cultural evolution}, volume={12}, ISSN={1520-6505}, url={http://dx.doi.org/10.1002/evan.10110}, DOI={10.1002/evan.10110}, number={3}, journal={Evolutionary Anthropology: Issues, News, and Reviews}, publisher={Wiley}, author={Henrich, Joseph and McElreath, Richard}, year={2003}, month=jan, pages={123–135} }
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Wolfgang Huber @wkhuber.bsky.social · 17/02/2024
Currently pondering novelty requirements by glamour methods / technology journals, both as an author and reviewer. There's an expectation to show that with the method you can do something that couldn't be done before. I understand the logic, but it strikes me, as an analogy, as ...
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NPR @npr.org · 12/02/2024
Live from NPR News, we’re now on Bluesky 👋🎙️
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Upbeat Former Prof @upbeatprof.bsky.social · 19/12/2023
Good to see people still take the T
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Lucas van Dijk @lucasvandijk.nl · 14/12/2023
I guess the Netherlands definitely counts as a tech hub these days: someone dedicated to the advent of code at 830am in the train, programming in Rust
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Lucas van Dijk @lucasvandijk.nl · 01/12/2023
Pretty crazy how effective modern hardware is at processing contiguous blocks of memory (e.g., a DP matrix) compared to for example graph traversal algorithms that have much more irregular computations.
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Ketan Joshi @ketanjoshi.co · 20/11/2023
this is a bloody great name for a climate report www.unep.org/resources/em...
Broken Record
Temperatures hit new highs, yet world fails to cut emissions (again)
UN
environment programme
。
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Lucas van Dijk @lucasvandijk.nl · 03/11/2023
Hard to believe he pleaded not guilty in the first place 🥲
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Chris Miller @chrismiller.science · 25/10/2023
I believe the field has landed on "Computeral Bioinfologist" @mikelove.bsky.social @robp.bsky.social
Chris Miller
I get that I'm not the arbiter of terminology but it all seems like meaningless distinctions to me. If you're using computers to study biological information, then  use any combination of those words as a title, Then more importantly, tell me what you *actually do*

Michael Love
so you're cool with me saying I study Computeral Bioinfology

Rob Patro
As long as you sound drunk whenever you say it, I’d be fine with this.
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