Reposted
"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."
The phenotypic variation of widefins medaka is due to the insertion of a giant transposon containing a viral genome within hoxca cluster
Abstract. Phenotypic variation in species arises from genetic differences and environmental influences on gene expression. Differences in epigenetic modifi
academic.oup.com
October 9, 2025 at 8:30 AM
"(...) an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the hoxc12a 3' UTR. This insertion decreased hoxc12a expression & (...) also affected neighboring hox genes, resulting in variations in fin size and the presence or absence of dorsal fins."
Reposted
SequencEnG: An interactive learning resource for next-generation sequencing (NGS) techniques education.knoweng.org/sequenceng/
It is impossible to be an expert of all those data types
but once you have the core solid foundation
you can learn how to analyze a new data type as needed
It is impossible to be an expert of all those data types
but once you have the core solid foundation
you can learn how to analyze a new data type as needed
October 7, 2025 at 1:45 PM
SequencEnG: An interactive learning resource for next-generation sequencing (NGS) techniques education.knoweng.org/sequenceng/
It is impossible to be an expert of all those data types
but once you have the core solid foundation
you can learn how to analyze a new data type as needed
It is impossible to be an expert of all those data types
but once you have the core solid foundation
you can learn how to analyze a new data type as needed
Reposted
tgv 0.1.0 release: github.com/zeqianli/tgv
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
September 7, 2025 at 11:47 PM
tgv 0.1.0 release: github.com/zeqianli/tgv
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
Reposted
Very happy to have contributed to this review on "non-CG" #methylation in animals now out in @natgenet.nature.com. Working again with @obog.bsky.social and Tirsa is always a pleasure. We think this not so well studied form of methylation should be more widely considered, please read: rdcu.be/eFAEk
Non-CG DNA methylation in animal genomes
Nature Genetics - This Review discusses noncanonical DNA methylation (mCH) in animal genomes and highlights the remaining need to clarify whether mCH represents a conserved regulatory layer or a...
rdcu.be
September 11, 2025 at 10:11 AM
Very happy to have contributed to this review on "non-CG" #methylation in animals now out in @natgenet.nature.com. Working again with @obog.bsky.social and Tirsa is always a pleasure. We think this not so well studied form of methylation should be more widely considered, please read: rdcu.be/eFAEk
Reposted
This recent paper shows "Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines"
www.nature.com/articles/s4...
I then saw PerturbNet from Josh Welch's group
x.com/labwelch/st...
www.nature.com/articles/s4...
I then saw PerturbNet from Josh Welch's group
x.com/labwelch/st...
August 6, 2025 at 2:15 PM
This recent paper shows "Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines"
www.nature.com/articles/s4...
I then saw PerturbNet from Josh Welch's group
x.com/labwelch/st...
www.nature.com/articles/s4...
I then saw PerturbNet from Josh Welch's group
x.com/labwelch/st...
Reposted
New tgv release: local cache!
tgv download hg38
Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple.
github.com/zeqianli/tgv
tgv download hg38
Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple.
github.com/zeqianli/tgv
GitHub - zeqianli/tgv: Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion.
Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv
github.com
July 19, 2025 at 11:37 PM
New tgv release: local cache!
tgv download hg38
Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple.
github.com/zeqianli/tgv
tgv download hg38
Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple.
github.com/zeqianli/tgv
Reposted
Published in today's issue! OPEN ACCESS article, FREE massive dataset, FREE code, FREE pre-trained AI/ML model. #OpenScience was a mountain of work to make this happen: check it out if you haven't already 😉
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
www.nature.com
March 13, 2025 at 7:32 PM
Published in today's issue! OPEN ACCESS article, FREE massive dataset, FREE code, FREE pre-trained AI/ML model. #OpenScience was a mountain of work to make this happen: check it out if you haven't already 😉