TFW a double helix interrupts your genotyping meeting
March 13, 2025 at 11:39 PM
TFW a double helix interrupts your genotyping meeting
@judgebove OKAY, PEOPLE. get ready for a THREAD about the RELIABILITY OF PROBABILISTIC GENOTYPING SOFTWARE 🧵
March 26, 2026 at 5:32 PM
@judgebove OKAY, PEOPLE. get ready for a THREAD about the RELIABILITY OF PROBABILISTIC GENOTYPING SOFTWARE 🧵
I found it surprisingly hard to find a simple visual explainer of the difference between genome sequencing, exome sequencing, and genotyping.
So I made one for this piece.
So I made one for this piece.
November 28, 2025 at 7:51 PM
I found it surprisingly hard to find a simple visual explainer of the difference between genome sequencing, exome sequencing, and genotyping.
So I made one for this piece.
So I made one for this piece.
@yekwah.bsky.social launches FlexIt: the S. flexneri genotyping scheme at @shigellameeting.bsky.social 🎉
April 21, 2026 at 12:41 PM
@yekwah.bsky.social launches FlexIt: the S. flexneri genotyping scheme at @shigellameeting.bsky.social 🎉
Anyway that was back in 1998 and since then Ancestry and 23andMe have made personal genotyping Big Business so I imagine this kind of drama is happening all the damned time now.
September 10, 2025 at 1:26 AM
Anyway that was back in 1998 and since then Ancestry and 23andMe have made personal genotyping Big Business so I imagine this kind of drama is happening all the damned time now.
We never used to say “doesn’t matter, people always got sick in hospitals”.
Never.
The attempts to prevent transmission even went as far as genotyping bugs to find the source.
Never.
The attempts to prevent transmission even went as far as genotyping bugs to find the source.
November 30, 2024 at 8:18 AM
We never used to say “doesn’t matter, people always got sick in hospitals”.
Never.
The attempts to prevent transmission even went as far as genotyping bugs to find the source.
Never.
The attempts to prevent transmission even went as far as genotyping bugs to find the source.
WHY did none of you tell me that ONE BATTLE AFTER ANOTHER features plot-critical onscreen electrophoresis-based genotyping???!!
October 26, 2025 at 3:30 AM
WHY did none of you tell me that ONE BATTLE AFTER ANOTHER features plot-critical onscreen electrophoresis-based genotyping???!!
I am currently innovating a top-tier gamer strat: vibes-based genotyping
September 25, 2026 at 8:45 AM
I am currently innovating a top-tier gamer strat: vibes-based genotyping
A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
The Great Genotyper: a graph-based method for population genotyping of small and structural variants
Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequenc...
pmc.ncbi.nlm.nih.gov
October 7, 2025 at 8:32 PM
A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
- there is almost no circumstance where MTHFR genotyping needs to be done because it doesn't change management, and most of the claimed disease associations for it are not supported.
- Folate receptor autoantibodies (FRAAs) ≠ cerebral folate deficiency
(5/7)
- Folate receptor autoantibodies (FRAAs) ≠ cerebral folate deficiency
(5/7)
September 28, 2025 at 8:16 PM
- there is almost no circumstance where MTHFR genotyping needs to be done because it doesn't change management, and most of the claimed disease associations for it are not supported.
- Folate receptor autoantibodies (FRAAs) ≠ cerebral folate deficiency
(5/7)
- Folate receptor autoantibodies (FRAAs) ≠ cerebral folate deficiency
(5/7)
Our paper was published today in Nature Biotech!
www.nature.com/articles/s41...
Tandem Repeat Genotyping Tool (TRGT) is a new method for genotyping tandem repeats in PacBio HiFi long reads. We used some nice algorithmic strategies to improve genotyping accuracy.
🖥️ 🧬
www.nature.com/articles/s41...
Tandem Repeat Genotyping Tool (TRGT) is a new method for genotyping tandem repeats in PacBio HiFi long reads. We used some nice algorithmic strategies to improve genotyping accuracy.
🖥️ 🧬
Characterization and visualization of tandem repeats at genome scale - Nature Biotechnology
A set of tools maps tandem repeats across complete genomes.
www.nature.com
January 2, 2024 at 5:45 PM
Our paper was published today in Nature Biotech!
www.nature.com/articles/s41...
Tandem Repeat Genotyping Tool (TRGT) is a new method for genotyping tandem repeats in PacBio HiFi long reads. We used some nice algorithmic strategies to improve genotyping accuracy.
🖥️ 🧬
www.nature.com/articles/s41...
Tandem Repeat Genotyping Tool (TRGT) is a new method for genotyping tandem repeats in PacBio HiFi long reads. We used some nice algorithmic strategies to improve genotyping accuracy.
🖥️ 🧬
Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n)
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling
AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu
doi.org
April 10, 2025 at 3:41 PM
Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n)
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
🦒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
Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/PacificBiosc...
April 11, 2025 at 3:30 PM
Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/PacificBiosc...
Population-wide single-pollen nuclei genotyping in #rye 🌾
Christina Waesch, et al.
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience #genomics
Christina Waesch, et al.
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience #genomics
November 4, 2025 at 2:45 AM
Population-wide single-pollen nuclei genotyping in #rye 🌾
Christina Waesch, et al.
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience #genomics
Christina Waesch, et al.
📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#PlantScience #genomics
pissing someone off but instead of them sending your own IP address to you, they start reading off your genotyping data
May 2, 2026 at 7:34 PM
pissing someone off but instead of them sending your own IP address to you, they start reading off your genotyping data
We’re unwrapping a new method today at @mskcancercenter.bsky.social. Led by Sydney Blattman, Nabih Maslah, and @austinv11.com with @danapeer.bsky.social, @ronanchaligne.bsky.social and @10xgenomics.bsky.social, we present GIFT: Genotyping In Fixed Transcriptomes www.biorxiv.org/content/10.6... 1/n
www.biorxiv.org
April 13, 2026 at 3:13 PM
We’re unwrapping a new method today at @mskcancercenter.bsky.social. Led by Sydney Blattman, Nabih Maslah, and @austinv11.com with @danapeer.bsky.social, @ronanchaligne.bsky.social and @10xgenomics.bsky.social, we present GIFT: Genotyping In Fixed Transcriptomes www.biorxiv.org/content/10.6... 1/n
Pre-phasing long reads improves structural variant genotyping. #LongReads #Sequencing #ReadsPhasing #StructuralVariants #Genotyping #Genomics #Bioinformatics
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
October 25, 2025 at 7:32 AM
Pre-phasing long reads improves structural variant genotyping. #LongReads #Sequencing #ReadsPhasing #StructuralVariants #Genotyping #Genomics #Bioinformatics
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping https://www.biorxiv.org/content/10.1101/2025.02.11.637720v1 🧬🖥️🧪 https://github.com/SchriderLab/TEforest
February 13, 2025 at 4:30 PM
Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping https://www.biorxiv.org/content/10.1101/2025.02.11.637720v1 🧬🖥️🧪 https://github.com/SchriderLab/TEforest
Good morning #ESEB2025, check out my poster P03.008 and discuss about how fishy is fish DNA, demography analysis, massive inversions, ultra-long ONT sequencing for de novo assemblies, structural variation genotyping…. and everything!
August 21, 2025 at 8:40 AM
Good morning #ESEB2025, check out my poster P03.008 and discuss about how fishy is fish DNA, demography analysis, massive inversions, ultra-long ONT sequencing for de novo assemblies, structural variation genotyping…. and everything!
Ji, Kapli, Flouri & @zihengyang.bsky.social assess the impact of genotyping errors in phylogenomic data on Bayesian inference of species trees, suggesting that it is better to sequence a few samples at high depths over many samples at low depths.
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model
Abstract. The multispecies coalescent (MSC) model accounts for genealogical fluctuations across the genome and provides a framework for analyzing genomic d
doi.org
August 19, 2025 at 7:35 PM
Ji, Kapli, Flouri & @zihengyang.bsky.social assess the impact of genotyping errors in phylogenomic data on Bayesian inference of species trees, suggesting that it is better to sequence a few samples at high depths over many samples at low depths.
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
Single-cell genotyping and transcriptomic analysis reveals cell-type specific and non-autonomous effects of mTOR pathway mutations in mosaic focal cortical dysplasia type II (FCDII) 🧠🧪
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Single-cell genotyping and transcriptomic profiling of mosaic focal cortical dysplasia - Nature Neuroscience
In this work, the authors performed a single-cell genotyping and transcriptomics analysis, revealing cell-type-specific and nonautonomous effects of mTOR pathway mutations in mosaic focal cortical dys...
www.nature.com
April 30, 2025 at 6:09 PM
Single-cell genotyping and transcriptomic analysis reveals cell-type specific and non-autonomous effects of mTOR pathway mutations in mosaic focal cortical dysplasia type II (FCDII) 🧠🧪
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
April 22, 2026 at 6:11 AM
Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
just need y’all to know that probabilistic genotyping using black box AI is being admitted as reliable DNA evidence in trials around the country
It’s worse than “getting things wrong.” It just makes shit up. In law, that’s a non-starter.
For instance, it’s one thing to inaccurately explain or analyze an existing case. What AI does is just make up from whole cloth the case!
Non starter technology when it does that.
For instance, it’s one thing to inaccurately explain or analyze an existing case. What AI does is just make up from whole cloth the case!
Non starter technology when it does that.
May 8, 2025 at 3:06 AM
just need y’all to know that probabilistic genotyping using black box AI is being admitted as reliable DNA evidence in trials around the country
New paper-based device boosts HIV test accuracy from dried blood samples
"Clinical evaluation of patterned dried plasma spot cards to support quantification of HIV viral load and reflexive genotyping"
www.pnas.org/doi/10.1073/...
"Clinical evaluation of patterned dried plasma spot cards to support quantification of HIV viral load and reflexive genotyping"
www.pnas.org/doi/10.1073/...
February 25, 2025 at 4:32 AM
New paper-based device boosts HIV test accuracy from dried blood samples
"Clinical evaluation of patterned dried plasma spot cards to support quantification of HIV viral load and reflexive genotyping"
www.pnas.org/doi/10.1073/...
"Clinical evaluation of patterned dried plasma spot cards to support quantification of HIV viral load and reflexive genotyping"
www.pnas.org/doi/10.1073/...