Lucas van Dijk @lucasvandijk.nl · 23/07/2026What a huge achievement! 450 human haplotypes. PacBio Kinnex transcriptomic data, Fiber-Seq (nucleosome occupancy), and so much more! 042
Lucas van Dijk @lucasvandijk.nl · 11/06/2026It’s really ridiculous how quickly it flags anything biology or bioinformatics 030
Reposted by Lucas van DijkPacBio @pacbio.bsky.social · 26/05/2026SPRQ-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 0147
Reposted by Lucas van DijkAlex Crits-Christoph @acritschristoph.bsky.social · 27/04/2026oh that's very very cool: 13410
Reposted by Lucas van DijkRichard McElreath 🐈⬛ @rmcelreath.bsky.social · 11/03/2026So 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. 1714421
Lucas van Dijk @lucasvandijk.nl · 30/11/2025That x86 ABI mug is going to be powering my mornings :) 140
Lucas van Dijk @lucasvandijk.nl · 28/11/2025I 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 😁 250
Reposted by Lucas van DijkMike Schatz @mikeschatz.bsky.social · 14/10/2025Getting 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.orgPheedLoopPheedLoop: Hybrid, In-Person & Virtual Event Software 1439
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.orgPopulation-scale Long-read Sequencing in the All of Us Research ProgramThe 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... 010
Reposted by Lucas van DijkErik Garrison @thinks.lol · 17/07/2025Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested! 12830
Reposted by Lucas van DijkAlexandria Ocasio-Cortez @aoc.bsky.social · 03/07/2025I 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. 34849983121746
Lucas van Dijk @lucasvandijk.nl · 11/02/2025And now officially out in Oxford Bioinformatics :) academic.oup.com/bioinformati...academic.oup.comFast and exact gap-affine partial order alignment with POASTAAbstractMotivation. Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pa 1131
Lucas van Dijk @lucasvandijk.nl · 09/02/2025For 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... 150
Lucas van Dijk @lucasvandijk.nl · 27/01/2025A printed thesis! Did not expect it would feel so good to have the final version physically in your hands 🙌 120
Reposted by Lucas van DijkNature Reviews Genetics @natrevgenet.nature.com · 27/01/2025Diversity 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.socialgo.nature.comDiversity and consequences of structural variation in the human genome - Nature Reviews GeneticsCollins 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... 2267
Reposted by Lucas van Dijkqntm @qntm.org · 17/01/2025COMPUTER SCIENTISTS: "k" means one thousand and twenty-four STORAGE MANUFACTURERS: "k" means one thousand DISPLAY MANUFACTURERS [thinking hard]: "K" means nine hundred and sixty 621811299
Reposted by Lucas van DijkTravis Wheeler @wheelerlab.org · 07/01/2025Still 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. 0115
Reposted by Lucas van DijkMing Tommy Tang @tommytang.bsky.social · 07/01/20255/ 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. 3192
Lucas van Dijk @lucasvandijk.nl · 25/11/2024Anyone insight how I can configure pylsp such that it finds and autocompletes packages installed with uv? 000
Lucas van Dijk @lucasvandijk.nl · 19/11/2024Found 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... 110
Reposted by Lucas van DijkBluesky @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.socialHow to set your domain as your handle - BlueskyUsing a domain as your handle helps with account identity, verification, and portability. Here's how to set your domain as your handle. 1445366396770
Lucas van Dijk @lucasvandijk.nl · 14/11/2024I 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? 131
Reposted by Lucas van DijkThibaut 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 26950186
Lucas van Dijk @lucasvandijk.nl · 12/11/2024I think Philip Eng deserves a statue in the Boston common 032
Lucas van Dijk @lucasvandijk.nl · 26/10/2024Working 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 🤯 010
Reposted by Lucas van DijkAlexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 10/10/2024The 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. !!!!! 14618
Lucas van Dijk @lucasvandijk.nl · 28/05/2024Excited 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.orgFast and exact gap-affine partial order alignment with POASTAbioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution 192
Reposted by Lucas van DijkJay 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.orgNew York Times editor Joe Kahn says defending democracy is a partisan act and he won’t do it | Press WatchJoe Kahn, after two years in charge of the New York Times newsroom, has learned nothing. 33375144
Reposted by Lucas van DijkStreetsblogMASS @mass.streetsblog.org · 23/04/2024Advocates Win Concessions As State Starts Value-Engineering Allston I-90 Megaprojectdlvr.itAdvocates Win Concessions As State Starts Value-Engineering Allston I-90 MegaprojectIn 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… 022
Reposted by Lucas van DijkHayes Brown @hayesbrown.bsky.social · 05/04/2024an earthquake three days before a total eclipse of the sun would absolutely have taken out a whole ass dynasty back in the day 9454741474
Reposted by Lucas van DijkRichard 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... 610626
Reposted by Lucas van DijkWolfgang Huber @wkhuber.bsky.social · 17/02/2024Currently 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 ... 195
Reposted by Lucas van DijkNPR @npr.org · 12/02/2024Live from NPR News, we’re now on Bluesky 👋🎙️ 38480141163
Reposted by Lucas van DijkUpbeat Former Prof @upbeatprof.bsky.social · 19/12/2023Good to see people still take the T 14704144
Lucas van Dijk @lucasvandijk.nl · 14/12/2023I 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 010
Lucas van Dijk @lucasvandijk.nl · 01/12/2023Pretty 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. 200
Reposted by Lucas van DijkKetan Joshi @ketanjoshi.co · 20/11/2023this is a bloody great name for a climate report www.unep.org/resources/em... 5442541611
Lucas van Dijk @lucasvandijk.nl · 03/11/2023Hard to believe he pleaded not guilty in the first place 🥲 030
Reposted by Lucas van DijkChris Miller @chrismiller.science · 25/10/2023I believe the field has landed on "Computeral Bioinfologist" @mikelove.bsky.social @robp.bsky.social 1286