@handstad.bsky.social
Reposted
GA4GH has approved the release of two new products: Experiments Metadata Checklist (Expmeta) and Whole Genome Sequencing Quality Control Standards (WGS QC)
Read more about the Expmeta: www.ga4gh.org/news_item/th...
Read more about WGS QC:
www.ga4gh.org/news_item/wh...
Read more about the Expmeta: www.ga4gh.org/news_item/th...
Read more about WGS QC:
www.ga4gh.org/news_item/wh...
November 13, 2025 at 2:58 PM
GA4GH has approved the release of two new products: Experiments Metadata Checklist (Expmeta) and Whole Genome Sequencing Quality Control Standards (WGS QC)
Read more about the Expmeta: www.ga4gh.org/news_item/th...
Read more about WGS QC:
www.ga4gh.org/news_item/wh...
Read more about the Expmeta: www.ga4gh.org/news_item/th...
Read more about WGS QC:
www.ga4gh.org/news_item/wh...
Reposted
Such a great @ga4gh.org meeting in Uppsala this past week. Genomics, with the help of GA4GH standards and policies, is really moving into the Age of Implementation globally!
October 11, 2025 at 4:26 AM
Such a great @ga4gh.org meeting in Uppsala this past week. Genomics, with the help of GA4GH standards and policies, is really moving into the Age of Implementation globally!
Reposted
This is a very good essay.
Now might be the best time to learn software development greenbluegray.substack.com/p/now-might-...
Now might be the best time to learn software development greenbluegray.substack.com/p/now-might-...
Now might be the best time to learn software development
And the most fun
greenbluegray.substack.com
June 19, 2025 at 9:48 PM
This is a very good essay.
Now might be the best time to learn software development greenbluegray.substack.com/p/now-might-...
Now might be the best time to learn software development greenbluegray.substack.com/p/now-might-...
Reposted
Reposted
🤗 Hugely excited to share our work on automating iterative reanalysis in #raredisease, preprint out: www.medrxiv.org/content/10.1... 🤖🧬
github.com/populationge...
A superb collaboration with @dgmacarthur.bsky.social @cassimons.bsky.social @heidirehm.bsky.social @ksamocha.bsky.social and many more!
github.com/populationge...
A superb collaboration with @dgmacarthur.bsky.social @cassimons.bsky.social @heidirehm.bsky.social @ksamocha.bsky.social and many more!
Scalable automated reanalysis of genomic data in research and clinical rare disease cohorts
Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necess...
www.medrxiv.org
May 23, 2025 at 6:04 AM
🤗 Hugely excited to share our work on automating iterative reanalysis in #raredisease, preprint out: www.medrxiv.org/content/10.1... 🤖🧬
github.com/populationge...
A superb collaboration with @dgmacarthur.bsky.social @cassimons.bsky.social @heidirehm.bsky.social @ksamocha.bsky.social and many more!
github.com/populationge...
A superb collaboration with @dgmacarthur.bsky.social @cassimons.bsky.social @heidirehm.bsky.social @ksamocha.bsky.social and many more!
Reposted
Release of DeepVariant and DeepSomatic v1.9
DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h).
DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.
github.com/google/deepv...
DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h).
DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.
github.com/google/deepv...
Release DeepVariant 1.9.0 · google/deepvariant
DeepVariant:
In this version we have updated our training scheme for the HG002 sample with the newly released HG002-T2T truth set which improves accuracy against that truth set.
Our labeling metho...
github.com
May 13, 2025 at 8:23 PM
Release of DeepVariant and DeepSomatic v1.9
DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h).
DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.
github.com/google/deepv...
DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h).
DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.
github.com/google/deepv...
Reposted
polars-bio - fast, scalable and out-of-core operations on large genomic interval datasets www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/biodatageeks...
March 26, 2025 at 9:37 AM
polars-bio - fast, scalable and out-of-core operations on large genomic interval datasets www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/biodatageeks...
Reposted
Looking forward to reading the new National Academies report -- The Age of AI in the Life Sciences: Benefits and Biosecurity Considerations 🧬🖥️🧪 nap.nationalacademies.org/catalog/2886...
March 14, 2025 at 8:01 PM
Looking forward to reading the new National Academies report -- The Age of AI in the Life Sciences: Benefits and Biosecurity Considerations 🧬🖥️🧪 nap.nationalacademies.org/catalog/2886...
Reposted
New preprint! We worked with @msftresearch.bsky.social and @broadinstitute.org to see whether large language models (LLMs) can be useful to variant scientists in deciding whether genetic variants seen in a patient are responsible for their disease. tl;dr yes they can: www.biorxiv.org/content/10.1...
Evidence Aggregator: AI reasoning applied to rare disease diagnostics
Retrieving, reviewing, and synthesizing technical information can be time-consuming and challenging, particularly when requiring specialized expertise, as is the case of variant assessment for rare di...
www.biorxiv.org
March 15, 2025 at 2:44 AM
New preprint! We worked with @msftresearch.bsky.social and @broadinstitute.org to see whether large language models (LLMs) can be useful to variant scientists in deciding whether genetic variants seen in a patient are responsible for their disease. tl;dr yes they can: www.biorxiv.org/content/10.1...
Reposted
We trained a genomic language model on all observed evolution, which we are calling Evo 2.
The model achieves an unprecedented breadth in capabilities, enabling prediction and design tasks from molecular to genome scale and across all three domains of life.
The model achieves an unprecedented breadth in capabilities, enabling prediction and design tasks from molecular to genome scale and across all three domains of life.
February 19, 2025 at 4:42 PM
We trained a genomic language model on all observed evolution, which we are calling Evo 2.
The model achieves an unprecedented breadth in capabilities, enabling prediction and design tasks from molecular to genome scale and across all three domains of life.
The model achieves an unprecedented breadth in capabilities, enabling prediction and design tasks from molecular to genome scale and across all three domains of life.
Recommendations for bioinformatics in clinical practice, from the Nordic Alliance of Clinical Genomics www.biorxiv.org/content/10.1...
Recommendations for Bioinformatics in Clinical Practice
Next Generation Sequencing (NGS) is increasingly used in clinical diagnostics, largely driven by the success and robustness of Whole Genome Sequencing (WGS). Whereas updated guidelines exist for how t...
www.biorxiv.org
November 26, 2024 at 9:02 PM
Recommendations for bioinformatics in clinical practice, from the Nordic Alliance of Clinical Genomics www.biorxiv.org/content/10.1...
Reposted
A vertical takeoff of life science with #AI LLLMs.
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...
November 24, 2024 at 6:12 PM
A vertical takeoff of life science with #AI LLLMs.
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...
Reposted
Genetic Discrimination Is Coming for Us All https://www.theatlantic.com/health/archive/2024/11/dna-genetic-discrimination-insurance-privacy/680626/
Unpaywalled: https://12ft.io/
Unpaywalled: https://12ft.io/
Genetic Discrimination Is Coming for Us All
Insurers are refusing to cover Americans whose DNA reveals health risks. It’s perfectly legal.
www.theatlantic.com
November 20, 2024 at 7:45 PM
Genetic Discrimination Is Coming for Us All https://www.theatlantic.com/health/archive/2024/11/dna-genetic-discrimination-insurance-privacy/680626/
Unpaywalled: https://12ft.io/
Unpaywalled: https://12ft.io/