Proud of this work, led by the amazing Jeannette Tenthorey (now Assistant Professor at UCSF), demonstrating the adaptive power of single indel mutations in host-virus arms races, but a little sad that this is the coda to her amazing postdoc in the Malik & Emerman labs.
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations
Tenthorey et al. compare the effects of missense and indel mutations on the acquisition
of functional novelty by the rapidly evolving antiviral protein TRIM5α. They find
that single indel mutations al...
www.cell.com
March 27, 2025 at 9:36 PM
Proud of this work, led by the amazing Jeannette Tenthorey (now Assistant Professor at UCSF), demonstrating the adaptive power of single indel mutations in host-virus arms races, but a little sad that this is the coda to her amazing postdoc in the Malik & Emerman labs.
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
the way im indel (involuntarily DL)
April 4, 2026 at 11:58 AM
the way im indel (involuntarily DL)
Indel, you dead buddy ☠️
January 8, 2025 at 10:53 PM
Indel, you dead buddy ☠️
Interviewer: Can you explain this gap in your resume?
That’s not a gap, it’s an Indel.
That’s not a gap, it’s an Indel.
Interviewer: Can you explain this gap in your resume?
What can I say, my toddler found the scissors.
What can I say, my toddler found the scissors.
Interviewer: Can you explain this gap in your resume?
Me: yeah, that's so all the text isn't jumbled together. Have you never read before?
Me: yeah, that's so all the text isn't jumbled together. Have you never read before?
December 21, 2024 at 8:10 PM
Interviewer: Can you explain this gap in your resume?
That’s not a gap, it’s an Indel.
That’s not a gap, it’s an Indel.
Who up glorfing they indel
January 2, 2026 at 9:47 AM
Who up glorfing they indel
What proportion of the sunflower genome has an indel in at least one individual? Basically all of it -- there's almost no sequence (at least at the 100kb window scale) found in all sunflowers!
April 8, 2026 at 4:33 PM
What proportion of the sunflower genome has an indel in at least one individual? Basically all of it -- there's almost no sequence (at least at the 100kb window scale) found in all sunflowers!
Who's gonna tell the genomes?
November 12, 2024 at 12:41 PM
Who's gonna tell the genomes?
In our new paper we characterize the effects of indel variants on protein folding and stability using a new yeast-based protein folding sensor. The work was led by Sven Larsen-Ledet and supported by the @novo-nordisk.bsky.social.
Link to paper: www.cell.com/structure/fu...
Link to paper: www.cell.com/structure/fu...
Systematic characterization of indel variants using a yeast-based protein folding sensor
Larsen-Ledet et al. developed a yeast-based protein folding sensor to determine the effects of indel variants in DHFR. Using a saturated indel library, it was found that most indels are not tolerated. Several are temperature sensitive and folding is rescued by methotrexate. Rosetta and AlphaFold2 predictions correlate with the observed effects.
www.cell.com
December 20, 2024 at 7:26 AM
In our new paper we characterize the effects of indel variants on protein folding and stability using a new yeast-based protein folding sensor. The work was led by Sven Larsen-Ledet and supported by the @novo-nordisk.bsky.social.
Link to paper: www.cell.com/structure/fu...
Link to paper: www.cell.com/structure/fu...
Moin und habt einen entspannten Sonntag ☕️ ☕️ ☕️
July 7, 2024 at 7:34 AM
Moin und habt einen entspannten Sonntag ☕️ ☕️ ☕️
A GWAS indicates that the leaf shape locus is on Chromosome 2, and coverage analyses indicate that it is a ~117 kb indel. The indel perfectly co-segregates with leaf shape. The indel is relatively close to two auxin-related genes implicated in leaf shape and development.
June 7, 2026 at 2:50 PM
A GWAS indicates that the leaf shape locus is on Chromosome 2, and coverage analyses indicate that it is a ~117 kb indel. The indel perfectly co-segregates with leaf shape. The indel is relatively close to two auxin-related genes implicated in leaf shape and development.
PAPER OUT!! 🥳🎉💃🏻🕺🏻💃🏻🕺🏻
A redefined InDel taxonomy provides insights into mutational signatures @NatureGenet
Brainchild of the amazing #GeneKoh
(Sir Jeffrey Cheah ECR)
Tweetorial below!! 👇
1/n
www.nature.com/articles/s41...
A redefined InDel taxonomy provides insights into mutational signatures @NatureGenet
Brainchild of the amazing #GeneKoh
(Sir Jeffrey Cheah ECR)
Tweetorial below!! 👇
1/n
www.nature.com/articles/s41...
A redefined InDel taxonomy provides insights into mutational signatures - Nature Genetics
This paper describes a framework for classifying small insertions and deletions from genomic data and applies it to a large dataset comprising seven tumor types. The analysis highlights new insertion ...
www.nature.com
April 10, 2025 at 4:48 PM
PAPER OUT!! 🥳🎉💃🏻🕺🏻💃🏻🕺🏻
A redefined InDel taxonomy provides insights into mutational signatures @NatureGenet
Brainchild of the amazing #GeneKoh
(Sir Jeffrey Cheah ECR)
Tweetorial below!! 👇
1/n
www.nature.com/articles/s41...
A redefined InDel taxonomy provides insights into mutational signatures @NatureGenet
Brainchild of the amazing #GeneKoh
(Sir Jeffrey Cheah ECR)
Tweetorial below!! 👇
1/n
www.nature.com/articles/s41...
Estimation of substitution and indel rates via k-mer statistics https://www.biorxiv.org/content/10.1101/2025.05.14.653858v1
May 18, 2025 at 4:48 AM
Estimation of substitution and indel rates via k-mer statistics https://www.biorxiv.org/content/10.1101/2025.05.14.653858v1
Weird indel in my reply, too…
August 9, 2025 at 12:03 AM
Weird indel in my reply, too…
Mandatory reading and surprising results from Michael Hall and colleagues - much better bacterial SNP/indel calling results from latest nanopore (beating illumina), and deep learning methods really doing well. Extremely thorough work
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
March 18, 2024 at 3:10 PM
Mandatory reading and surprising results from Michael Hall and colleagues - much better bacterial SNP/indel calling results from latest nanopore (beating illumina), and deep learning methods really doing well. Extremely thorough work
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The hotel minibar matches the topic of the thesis ("The impact of amino acid insertions and deletions on protein stability and function")
January 8, 2025 at 6:26 PM
The hotel minibar matches the topic of the thesis ("The impact of amino acid insertions and deletions on protein stability and function")
⚡️ Our latest preprint is on bioRxiv!
Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
Shift augmentation improves DNA convolutional neural network indel effect predictions
Determining genetic variant effects on molecular phenotypes like gene expression is a task of paramount importance to medical genetics. DNA convolutional neural networks (CNNs) attain state-of-the-art...
www.biorxiv.org
April 16, 2025 at 9:13 PM
⚡️ Our latest preprint is on bioRxiv!
Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
Benchmarking by Harvey et al. shows PacBio HiFi achieves higher indel & SV recall at 20x than ONT achieves at 60x+. 📊
Citing the right peer-reviewed data is key to a winning grant proposal. See how our literature library helps you write yours faster: https://bit.ly/4ycWZ3q
Citing the right peer-reviewed data is key to a winning grant proposal. See how our literature library helps you write yours faster: https://bit.ly/4ycWZ3q
September 23, 2026 at 6:49 PM
Benchmarking by Harvey et al. shows PacBio HiFi achieves higher indel & SV recall at 20x than ONT achieves at 60x+. 📊
Citing the right peer-reviewed data is key to a winning grant proposal. See how our literature library helps you write yours faster: https://bit.ly/4ycWZ3q
Citing the right peer-reviewed data is key to a winning grant proposal. See how our literature library helps you write yours faster: https://bit.ly/4ycWZ3q
Added SPRQ to PacBio training, reducing Indel error on SPRQ by 26%. Added Platinum Pedigree training data for PacBio model, reducing errors by 34% on more extensive Platinum truth. New model and case study for Kinnex/Mas-Seq/Iso-Seq. Additional speed options for GPU pipelines 2/3
December 5, 2024 at 5:57 PM
Added SPRQ to PacBio training, reducing Indel error on SPRQ by 26%. Added Platinum Pedigree training data for PacBio model, reducing errors by 34% on more extensive Platinum truth. New model and case study for Kinnex/Mas-Seq/Iso-Seq. Additional speed options for GPU pipelines 2/3
Resurrecting Full-length Ancestral Schizorhodopsins and Heliorhodopsins with Structure-guided, Indel-aware Sequence Reconstruction www.biorxiv.org/content/10.6...
March 12, 2026 at 7:43 AM
Resurrecting Full-length Ancestral Schizorhodopsins and Heliorhodopsins with Structure-guided, Indel-aware Sequence Reconstruction www.biorxiv.org/content/10.6...
A Structure-guided, Indel-aware Framework for Ancestral Reconstruction of Full-length Seven-transmembrane Proteins www.biorxiv.org/content/10.6...
December 31, 2025 at 6:10 AM
A Structure-guided, Indel-aware Framework for Ancestral Reconstruction of Full-length Seven-transmembrane Proteins www.biorxiv.org/content/10.6...
We have known for a long time that CRISPR works - gene editing - “traditional” indel inducing, base editing and funkier types. We have a set of traits in a set of organisms where we know causal genes or alleles, and the consequences of knockouts.
April 8, 2025 at 6:57 AM
We have known for a long time that CRISPR works - gene editing - “traditional” indel inducing, base editing and funkier types. We have a set of traits in a set of organisms where we know causal genes or alleles, and the consequences of knockouts.
Lots of debate about the infamous furin cleavage site (FCS) in SARS-CoV-2 and it's alleged uniqueness. But Paul Bieniasz see "numerous examples of potential FCS acquisition...during normal coronavirus replication", concluding "such events are likely commonplace".
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Genetic innovation in coronaviruses driven by a viral nuclease
Genetic variation in viruses is well known to arise from polymerase-driven nucleotide misincorporation. However, insertion and deletion (indel) mutations that occur at lower, largely unknown, frequenc...
www.biorxiv.org
August 18, 2026 at 9:34 PM
Lots of debate about the infamous furin cleavage site (FCS) in SARS-CoV-2 and it's alleged uniqueness. But Paul Bieniasz see "numerous examples of potential FCS acquisition...during normal coronavirus replication", concluding "such events are likely commonplace".
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
What indels you get at a Cas9 cut site depends on the flanking sequence and the proteins that repair the break. Paper below analyses how different repair factors influence the frequency of indel types.
#CRISPR
#CRISPR
www.nature.com/articles/s41... A collaborative project incepted by Michael Kosicki, and executed by Ananth Pallaseni (both Ph.D students at @sangerinstitute.bsky.social at the time) and Elin-Madli Peets.
The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations - Nature Communications
Here the authors measure how the absence of certain DNA repair genes change the frequencies of unique mutational outcomes generated by Cas9 DSBs at synthetic target sequences in mouse embryonic stem c...
www.nature.com
November 28, 2024 at 7:39 AM
What indels you get at a Cas9 cut site depends on the flanking sequence and the proteins that repair the break. Paper below analyses how different repair factors influence the frequency of indel types.
#CRISPR
#CRISPR
My amazing pal Gene Koh strikes again! #InDel #CancerGenomics #MutationalSignatures @naturegenet.bsky.social
PAPER OUT!! 🥳🎉💃🏻🕺🏻💃🏻🕺🏻
A redefined InDel taxonomy provides insights into mutational signatures @NatureGenet
Brainchild of the amazing #GeneKoh
(Sir Jeffrey Cheah ECR)
Tweetorial below!! 👇
1/n
www.nature.com/articles/s41...
A redefined InDel taxonomy provides insights into mutational signatures @NatureGenet
Brainchild of the amazing #GeneKoh
(Sir Jeffrey Cheah ECR)
Tweetorial below!! 👇
1/n
www.nature.com/articles/s41...
A redefined InDel taxonomy provides insights into mutational signatures - Nature Genetics
This paper describes a framework for classifying small insertions and deletions from genomic data and applies it to a large dataset comprising seven tumor types. The analysis highlights new insertion ...
www.nature.com
April 11, 2025 at 9:34 PM
My amazing pal Gene Koh strikes again! #InDel #CancerGenomics #MutationalSignatures @naturegenet.bsky.social