Lucas van Dijk
@lucasvandijk.nl
Bioinformatics scientist at the Broad Institute 🖥️🧬. I am working on (pangenome) graph alignment and machine learning algorithms for identifying multi-omic QTLs in the All of Us Biobank.
Reposted by Lucas van Dijk
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...
PheedLoop
PheedLoop: Hybrid, In-Person & Virtual Event Software
meetings.ashg.org
October 14, 2025 at 5:40 PM
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...
>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...
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...
www.medrxiv.org
October 7, 2025 at 3:41 PM
>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...
Reposted by Lucas van Dijk
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
July 17, 2025 at 7:53 AM
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
Reposted by Lucas van Dijk
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.
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.
July 3, 2025 at 8:00 PM
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.
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.
The efficiency of the market
As a reference, the $46B that Meta spent building this shit is about the same amount of money Spain used to built its WHOLE high speed rail network.
All 2469 miles of it.
Zuckerberg got that money selling shitty ads and destroying democracy, and gave the world this.
All 2469 miles of it.
Zuckerberg got that money selling shitty ads and destroying democracy, and gave the world this.
This is Meta’s brand new ad for Horizon Worlds. Not sure how I’m supposed to feel about it.
February 17, 2025 at 2:28 PM
The efficiency of the market
What the actual fuck is this
This is Meta’s brand new ad for Horizon Worlds. Not sure how I’m supposed to feel about it.
February 17, 2025 at 2:27 PM
What the actual fuck is this
February 11, 2025 at 2:24 AM
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...
Installable through the Zed extensions pane!
github.com/broadinstitu...
February 9, 2025 at 10:04 PM
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...
Installable through the Zed extensions pane!
github.com/broadinstitu...
A printed thesis! Did not expect it would feel so good to have the final version physically in your hands 🙌
January 27, 2025 at 2:54 PM
A printed thesis! Did not expect it would feel so good to have the final version physically in your hands 🙌
Reposted by Lucas van Dijk
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
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...
go.nature.com
January 27, 2025 at 12:17 PM
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
Reposted by Lucas van Dijk
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
STORAGE MANUFACTURERS: "k" means one thousand
DISPLAY MANUFACTURERS [thinking hard]: "K" means nine hundred and sixty
January 17, 2025 at 10:34 PM
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
STORAGE MANUFACTURERS: "k" means one thousand
DISPLAY MANUFACTURERS [thinking hard]: "K" means nine hundred and sixty
Reposted by Lucas van Dijk
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.
Low mem construction. Spaced seeds. Optional crazy-low-mem search. More info on the horizon.
I've pushed a new version of Sufr, a #Rust implementation for fast parallel creation and searching of a suffix array. This release includes support for spaced seeds and searches requiring almost no RAM.
crates.io/crates/sufr
crates.io/crates/sufr
crates.io: Rust Package Registry
crates.io
January 7, 2025 at 11:39 PM
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.
Low mem construction. Spaced seeds. Optional crazy-low-mem search. More info on the horizon.
Reposted by Lucas van Dijk
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.
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.
January 7, 2025 at 2:15 PM
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.
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.
Anyone insight how I can configure pylsp such that it finds and autocompletes packages installed with uv?
November 25, 2024 at 3:59 AM
Anyone insight how I can configure pylsp such that it finds and autocompletes packages installed with uv?
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...
"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...
November 19, 2024 at 7:47 PM
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...
"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...
Reposted by Lucas van Dijk
💡 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:
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:
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.
bsky.social
November 15, 2024 at 10:04 PM
💡 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:
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:
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?
I'll start: Did you know that changing the number of threads used by bwa-mem can influence your BAM output?
November 14, 2024 at 4:08 PM
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?
I'll start: Did you know that changing the number of threads used by bwa-mem can influence your BAM output?
Reposted by Lucas van Dijk
[looking at Bluesky over the past 2 days] So this is what the Cambrian explosion must have felt like
November 11, 2024 at 10:17 PM
[looking at Bluesky over the past 2 days] So this is what the Cambrian explosion must have felt like
I think Philip Eng deserves a statue in the Boston common
November 12, 2024 at 1:08 PM
I think Philip Eng deserves a statue in the Boston common
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 🤯
October 26, 2024 at 3:48 PM
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 🤯
Reposted by Lucas van Dijk
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. !!!!!
go go @lindorfflarsen.bsky.social and col. !!!!!
October 10, 2024 at 9:29 AM
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. !!!!!
go go @lindorfflarsen.bsky.social and col. !!!!!
Reposted by Lucas van Dijk
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...
www.biorxiv.org/content/10.1...
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
www.biorxiv.org
May 28, 2024 at 5:27 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Lucas van Dijk
"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-...
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-...
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.
presswatchers.org
May 8, 2024 at 4:01 PM
"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-...
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-...
Reposted by Lucas van Dijk
Advocates Win Concessions As State Starts Value-Engineering Allston I-90 Megaproject
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…
dlvr.it
April 22, 2024 at 11:42 PM
Advocates Win Concessions As State Starts Value-Engineering Allston I-90 Megaproject