Wen-Wei Liao
@wwliao.bsky.social
Postdoctoral Associate at Yale University
https://medicine.yale.edu/profile/wen-wei-liao
https://medicine.yale.edu/profile/wen-wei-liao
Just found out #Nextflow supports job arrays 😅
Add `array` inside the `process { ... }` block, and it fixes “You have reached the rate limit of jobs submitted per hour” error.
Add `array
November 5, 2025 at 9:16 PM
Just found out #Nextflow supports job arrays 😅
Add `array` inside the `process { ... }` block, and it fixes “You have reached the rate limit of jobs submitted per hour” error.
Add `array
Reposted by Wen-Wei Liao
Locityper enables targeted genotyping of complex polymorphic genes www.nature.com/articles/s41... (🔓https://rdcu.be/eLxCC) 🧬🖥️🧪 github.com/tprodanov/lo...
October 21, 2025 at 5:55 PM
Locityper enables targeted genotyping of complex polymorphic genes www.nature.com/articles/s41... (🔓https://rdcu.be/eLxCC) 🧬🖥️🧪 github.com/tprodanov/lo...
Reposted by Wen-Wei Liao
I’ll be presenting a poster on Mitorsaw for #PacBio HiFi mitochondrial analysis today! Come see me this afternoon at #ASHG25 poster #4050 to chat about that or other topics!
I'm heading to Boston for #ASHG25 tomorrow, let me know if you'd like to chat about using HiFi sequencing for mitochondrial analyses, pharmacogenomics, or anything else!
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
October 17, 2025 at 11:48 AM
Reposted by Wen-Wei Liao
In honor of ASHG week (since I won’t be there), see "Choose your human genome reference wisely", in which Vivien Marx interviewed me @fergalmartin.bsky.social @lh3lh3.bsky.social @danrdanny.bsky.social @heidirehm.bsky.social and others on the state of the human reference rdcu.be/eJejg 🧵[1/10]
October 13, 2025 at 8:14 PM
In honor of ASHG week (since I won’t be there), see "Choose your human genome reference wisely", in which Vivien Marx interviewed me @fergalmartin.bsky.social @lh3lh3.bsky.social @danrdanny.bsky.social @heidirehm.bsky.social and others on the state of the human reference rdcu.be/eJejg 🧵[1/10]
Reposted by Wen-Wei Liao
After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)
Efficient and accurate search in petabase-scale sequence repositories - Nature
MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.
www.nature.com
October 8, 2025 at 8:56 PM
After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)
Reposted by Wen-Wei Liao
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Staff Scientist
About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...
embl.wd103.myworkdayjobs.com
October 10, 2025 at 7:30 AM
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Wen-Wei Liao
Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 10, 2025 at 1:02 PM
Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬
Reposted by Wen-Wei Liao
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
October 6, 2025 at 8:07 PM
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Reposted by Wen-Wei Liao
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1
October 2, 2025 at 6:28 AM
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Reposted by Wen-Wei Liao
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
September 30, 2025 at 2:19 AM
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
Reposted by Wen-Wei Liao
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
Reposted by Wen-Wei Liao
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
September 12, 2025 at 7:00 PM
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
Reposted by Wen-Wei Liao
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Phishing site : minimap2.com · Issue #1316 · lh3/minimap2
Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...
github.com
September 9, 2025 at 3:40 PM
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Reposted by Wen-Wei Liao
Now published in GigaScience with minor improvements: academic.oup.com/gigascience/...
* Download: zenodo.org/records/1490...
* More info: github.com/lh3/panmask
* Download: zenodo.org/records/1490...
* More info: github.com/lh3/panmask
Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718
September 4, 2025 at 4:44 PM
Now published in GigaScience with minor improvements: academic.oup.com/gigascience/...
* Download: zenodo.org/records/1490...
* More info: github.com/lh3/panmask
* Download: zenodo.org/records/1490...
* More info: github.com/lh3/panmask
Reposted by Wen-Wei Liao
GBZ-base has been a side project for me for a couple of years. It's basically a GBZ graph stored in SQLite instead of a custom file format. You can convert a GBZ graph to GBZ-base quickly and then extract subgraphs around nodes / reference positions on a laptop. 1/n
GitHub - jltsiren/gbz-base: Prototype for an immutable pangenome graph in SQLite
Prototype for an immutable pangenome graph in SQLite - jltsiren/gbz-base
github.com
August 28, 2025 at 12:49 AM
GBZ-base has been a side project for me for a couple of years. It's basically a GBZ graph stored in SQLite instead of a custom file format. You can convert a GBZ graph to GBZ-base quickly and then extract subgraphs around nodes / reference positions on a laptop. 1/n
Reposted by Wen-Wei Liao
August 15, 2025 at 5:19 PM
Reposted by Wen-Wei Liao
The Sudmant lab at UC Berkeley is seeking a postdoc to work on a fully funded NIH project to understand differences in DNA repair and somatic mutation across the primate tree of life. Please spread widely to those who may be interested aprecruit.berkeley.edu/JPF05052
Postdoctoral Scholar – Genomics, Aging, Somatic Mutation, Structural Variation, Evolution , Cancer – Integrative Biology
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
August 13, 2025 at 4:22 AM
The Sudmant lab at UC Berkeley is seeking a postdoc to work on a fully funded NIH project to understand differences in DNA repair and somatic mutation across the primate tree of life. Please spread widely to those who may be interested aprecruit.berkeley.edu/JPF05052
Reposted by Wen-Wei Liao
Good discussion & study-design recommendations in this new preprint by @mikelove.bsky.social @klmohlke.bsky.social & colleagues:
Higher eQTL power reveals signals that boost GWAS colocalization 🧪🧬
www.biorxiv.org/content/10.1...
Higher eQTL power reveals signals that boost GWAS colocalization 🧪🧬
www.biorxiv.org/content/10.1...
Higher eQTL power reveals signals that boost GWAS colocalization
Expression quantitative trait locus (eQTL) studies in human cohorts typically detect at least one regulatory signal per gene, and have been proposed as a way to explain mechanisms of genetic liability...
www.biorxiv.org
August 6, 2025 at 12:45 PM
Good discussion & study-design recommendations in this new preprint by @mikelove.bsky.social @klmohlke.bsky.social & colleagues:
Higher eQTL power reveals signals that boost GWAS colocalization 🧪🧬
www.biorxiv.org/content/10.1...
Higher eQTL power reveals signals that boost GWAS colocalization 🧪🧬
www.biorxiv.org/content/10.1...
Reposted by Wen-Wei Liao
This sounds true to me
!["When you vibe code, you are incurring tech debt as fast as the LLM can spit it out.
Which is why vibe coding is perfect for prototypes and throwaway projects: It'
s only
legacy code if you have to maintain it! !...]
The worst possible situation is to have a non-programmer vibe code a large project that they intend to maintain. This would be the equivalent of giving a credit card to a child without first explaining the concept of debt. [...]"](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:gxxr4j7mf2sc3ebakcghqm6p/bafkreiehhrnrupyuwkvewpvj22ozapeqpwtyvs43plc4yseyvda4vt4qem@jpeg)
August 5, 2025 at 10:34 AM
This sounds true to me
Reposted by Wen-Wei Liao
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
August 4, 2025 at 1:52 PM
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
Reposted by Wen-Wei Liao
Writing a technical blog improves your writing, forces you to learn new things, helps others and yourself, and helps your career. In this essay: (1) why blog, (2) what to blog about, (3) how to get started, and (4) using AI. https://doi.org/10.59350/bqnfd-7p249 🧪
Technical blogging for growth and learning
Writing a technical blog improves your writing, forces you to learn new things, helps others and yourself, and helps your career. This post: why blog, what to blog about, how to start, and using AI.
doi.org
January 25, 2025 at 4:00 PM
Writing a technical blog improves your writing, forces you to learn new things, helps others and yourself, and helps your career. In this essay: (1) why blog, (2) what to blog about, (3) how to get started, and (4) using AI. https://doi.org/10.59350/bqnfd-7p249 🧪
Reposted by Wen-Wei Liao
Complete genomes alert! @glennislogsdon.bsky.social, @christinebeck.bsky.social, and I were on @scifri.bsky.social today talking about "Complex genetic variation in nearly complete human genomes"
📄 www.nature.com/articles/s41...
📻 www.sciencefriday.com/segments/65-...
📄 www.nature.com/articles/s41...
📻 www.sciencefriday.com/segments/65-...
65 Genomes Expand Our Picture Of Human Genetics
Researchers closely examined the genomes of 65 individuals to paint a more complex, and more complete, picture of human genetic diversity.
www.sciencefriday.com
August 1, 2025 at 8:49 PM
Complete genomes alert! @glennislogsdon.bsky.social, @christinebeck.bsky.social, and I were on @scifri.bsky.social today talking about "Complex genetic variation in nearly complete human genomes"
📄 www.nature.com/articles/s41...
📻 www.sciencefriday.com/segments/65-...
📄 www.nature.com/articles/s41...
📻 www.sciencefriday.com/segments/65-...
Reposted by Wen-Wei Liao
Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions.
github.com/lh3/longdust
github.com/lh3/longdust
GitHub - lh3/longdust: Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome
Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome - lh3/longdust
github.com
July 31, 2025 at 7:59 PM
Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions.
github.com/lh3/longdust
github.com/lh3/longdust
Reposted by Wen-Wei Liao
Two papers in today's issue of @nature.com : 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.
Complex genetic variation in nearly complete human genomes - Nature
Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.
tinyurl.com
July 23, 2025 at 3:12 PM
Two papers in today's issue of @nature.com : 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.
Reposted by Wen-Wei Liao
Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718
July 8, 2025 at 2:14 AM
Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718