Legend of Dragoon - Bale & Indels Castle. gotta love pre-rendered house cutouts from this era!
April 18, 2025 at 12:25 PM
Legend of Dragoon - Bale & Indels Castle. gotta love pre-rendered house cutouts from this era!
InDels (Insertionen oder Deletionen) sind Basenpaare die zusätzlich eingebaut sind oder fehlen. Ist deren Zahl klein und nicht durch 3 teilbar (immer 3 Basen kodieren eine Aminosäure), dann verschieben InDels den gesamten Leserahmen eines Gens und das ergibt in der Regel völligen Unsinn und
6/17
6/17
January 6, 2025 at 6:40 AM
InDels (Insertionen oder Deletionen) sind Basenpaare die zusätzlich eingebaut sind oder fehlen. Ist deren Zahl klein und nicht durch 3 teilbar (immer 3 Basen kodieren eine Aminosäure), dann verschieben InDels den gesamten Leserahmen eines Gens und das ergibt in der Regel völligen Unsinn und
6/17
6/17
also two students chose cookies as their project medium, which is always highly encouraged
(one decorated some with types of mutations- indels, substitutions, etc- and the other did an elaborate set of Punnett squares for diff recipes and then used her family members to enact natural selection lol)
(one decorated some with types of mutations- indels, substitutions, etc- and the other did an elaborate set of Punnett squares for diff recipes and then used her family members to enact natural selection lol)
December 11, 2025 at 10:26 PM
also two students chose cookies as their project medium, which is always highly encouraged
(one decorated some with types of mutations- indels, substitutions, etc- and the other did an elaborate set of Punnett squares for diff recipes and then used her family members to enact natural selection lol)
(one decorated some with types of mutations- indels, substitutions, etc- and the other did an elaborate set of Punnett squares for diff recipes and then used her family members to enact natural selection lol)
Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations @harmitmalik.bsky.social
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
March 27, 2025 at 4:18 AM
Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations @harmitmalik.bsky.social
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Kickstarting our Bluesky🦋 account with great news!
Our REPAIRome study finally out today in
@science.org
www.science.org/doi/10.1126/...
Our REPAIRome study finally out today in
@science.org
www.science.org/doi/10.1126/...
A comprehensive genetic catalog of human double-strand break repair
The analysis of DNA sequence outcomes provides molecular insights into double-strand break (DSB) repair mechanisms. Using parallel in-pool profiling of Cas9-induced insertions and deletions (indels) w...
www.science.org
October 4, 2025 at 7:27 AM
Kickstarting our Bluesky🦋 account with great news!
Our REPAIRome study finally out today in
@science.org
www.science.org/doi/10.1126/...
Our REPAIRome study finally out today in
@science.org
www.science.org/doi/10.1126/...
QuickVariants 🦠🧬🧪- a genetic variant identification tool developed for microbes, now on Bioconda! 🚀
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
Fast and accurate variant identification tool for sequencing-based studies - BMC Biology
Background Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, a...
bmcbiol.biomedcentral.com
September 18, 2025 at 10:02 AM
QuickVariants 🦠🧬🧪- a genetic variant identification tool developed for microbes, now on Bioconda! 🚀
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
Short insertions and deletions are abundant but are they useful markers in genome scans for divergent selection? Hybrid zones in Littorina suggest they can add to information from SNPs, despite stronger purifying selection:
doi.org/10.1093/jeb/...
Perini, Butlin and @anjamwestram.bsky.social
doi.org/10.1093/jeb/...
Perini, Butlin and @anjamwestram.bsky.social
Short INDELs and SNPs as markers of evolutionary processes in hybrid zones
Abstract. Polymorphic short insertions and deletions (INDELs ≤ 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evide
doi.org
February 20, 2025 at 1:04 PM
Short insertions and deletions are abundant but are they useful markers in genome scans for divergent selection? Hybrid zones in Littorina suggest they can add to information from SNPs, despite stronger purifying selection:
doi.org/10.1093/jeb/...
Perini, Butlin and @anjamwestram.bsky.social
doi.org/10.1093/jeb/...
Perini, Butlin and @anjamwestram.bsky.social
Excited to share my main PhD work is finally out! 🥳
We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)!
See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞
We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)!
See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞
Phage-Assisted Evolution of Allosteric Protein Switches https://www.biorxiv.org/content/10.1101/2025.06.12.659331v1
June 13, 2025 at 9:23 AM
Excited to share my main PhD work is finally out! 🥳
We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)!
See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞
We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)!
See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞
My pick for In Other Journals this week:
Prime editing facilitates engineering of large indels in plants www.science.org/doi/10.1126/...
doi.org/10.1038/s414...
#PlantScience
Prime editing facilitates engineering of large indels in plants www.science.org/doi/10.1126/...
doi.org/10.1038/s414...
#PlantScience
In Other Journals
Editors’ selections from the current scientific literature
www.science.org
February 14, 2025 at 9:56 AM
My pick for In Other Journals this week:
Prime editing facilitates engineering of large indels in plants www.science.org/doi/10.1126/...
doi.org/10.1038/s414...
#PlantScience
Prime editing facilitates engineering of large indels in plants www.science.org/doi/10.1126/...
doi.org/10.1038/s414...
#PlantScience
Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Multiplex generation and single-cell analysis of structural variants in mammalian genomes
Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) ...
www.science.org
January 31, 2025 at 7:41 PM
Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
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...
TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data. #LongReads #Sequencing #SVs #TRs #CNVs #Indels #Bioinformatics #Sequencing #GenomeBiology 🧬 🖥️
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
September 1, 2025 at 5:06 PM
TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data. #LongReads #Sequencing #SVs #TRs #CNVs #Indels #Bioinformatics #Sequencing #GenomeBiology 🧬 🖥️
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
A comprehensive genetic catalog of human double-strand break repair | Science www.science.org/doi/10.1126/...
A comprehensive genetic catalog of human double-strand break repair
The analysis of DNA sequence outcomes provides molecular insights into double-strand break (DSB) repair mechanisms. Using parallel in-pool profiling of Cas9-induced insertions and deletions (indels) w...
www.science.org
October 2, 2025 at 6:47 PM
A comprehensive genetic catalog of human double-strand break repair | Science www.science.org/doi/10.1126/...
How to measure bacterial genome plasticity? A novel index helps gather insights on pathogens. Find out more in MGen: doi.org/10.1099/mgen... #MGen
September 5, 2025 at 11:01 AM
How to measure bacterial genome plasticity? A novel index helps gather insights on pathogens. Find out more in MGen: doi.org/10.1099/mgen... #MGen
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
Ha! No. But gloves are off when there are indels / CNVs …
September 1, 2025 at 10:21 PM
Ha! No. But gloves are off when there are indels / CNVs …
To make sure evolution actually happened in our finalist strains, we whole-genome sequenced them and discovered many interesting mutations: aneuploidies, large chromosomal rearrangements, point mutations, indels, and loss-of-heterozygosity (LOH) events.
September 22, 2026 at 6:34 PM
To make sure evolution actually happened in our finalist strains, we whole-genome sequenced them and discovered many interesting mutations: aneuploidies, large chromosomal rearrangements, point mutations, indels, and loss-of-heterozygosity (LOH) events.
Believe it or not, Littorina 🐚 not only have the SNPs and inversions we talk about all the time, but also indels! 🧬 For his PhD, Samuel Perini analysed them and asked whether they could be used as markers just like SNPs. The answer is... in the paper.
#Evolution
#Genomics
#Snails
#Evolution
#Genomics
#Snails
Short insertions and deletions are abundant but are they useful markers in genome scans for divergent selection? Hybrid zones in Littorina suggest they can add to information from SNPs, despite stronger purifying selection:
doi.org/10.1093/jeb/...
Perini, Butlin and @anjamwestram.bsky.social
doi.org/10.1093/jeb/...
Perini, Butlin and @anjamwestram.bsky.social
Short INDELs and SNPs as markers of evolutionary processes in hybrid zones
Abstract. Polymorphic short insertions and deletions (INDELs ≤ 50 bp) are abundant, although less common than single nucleotide polymorphisms (SNPs). Evide
doi.org
February 23, 2025 at 9:08 PM
Believe it or not, Littorina 🐚 not only have the SNPs and inversions we talk about all the time, but also indels! 🧬 For his PhD, Samuel Perini analysed them and asked whether they could be used as markers just like SNPs. The answer is... in the paper.
#Evolution
#Genomics
#Snails
#Evolution
#Genomics
#Snails
"BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels."
Sensitive and error-tolerant annotation of protein-coding DNA with BATH https://www.biorxiv.org/content/10.1101/2023.12.31.573773v1
Sensitive and error-tolerant annotation of protein-coding DNA with BATH https://www.biorxiv.org/content/10.1101/2023.12.31.573773v1
We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignm
www.biorxiv.org
January 2, 2024 at 8:51 AM
"BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels."
I'm giving a seminar on the state of ML for modeling protein dynamics & would love to hear some examples of elegant, well-designed studies that use MD to answer insightful biological questions. Especially those that look at the effects of ligands or mutations (incl indels) on energy landscapes, etc
March 11, 2025 at 8:39 AM
I'm giving a seminar on the state of ML for modeling protein dynamics & would love to hear some examples of elegant, well-designed studies that use MD to answer insightful biological questions. Especially those that look at the effects of ligands or mutations (incl indels) on energy landscapes, etc
What do people use to align somewhat distant related viral genes?
I'm working on somewhat distantly related viruses (i.e. across the Iridoviridae) and there is high divergence and a lot of indels.
🧪
I'm working on somewhat distantly related viruses (i.e. across the Iridoviridae) and there is high divergence and a lot of indels.
🧪
September 13, 2024 at 5:48 AM
What do people use to align somewhat distant related viral genes?
I'm working on somewhat distantly related viruses (i.e. across the Iridoviridae) and there is high divergence and a lot of indels.
🧪
I'm working on somewhat distantly related viruses (i.e. across the Iridoviridae) and there is high divergence and a lot of indels.
🧪
Evolution of ultraconserved elements by indels https://www.biorxiv.org/content/10.1101/2025.05.27.656252v1
May 29, 2025 at 8:32 PM
Evolution of ultraconserved elements by indels https://www.biorxiv.org/content/10.1101/2025.05.27.656252v1
Checkout our latest in @nature.com Integrated Mutational Footprints (SBS+Indels+SV+CIN signatures) define the mutational processes shaping 85% of prostate cancer genomes and outcomes. Explainer 👇
1/ NEW PAPER 🎉
🧵 We mapped the mutational processes shaping 959 prostate cancer genomes from the Pan Prostate Cancer Group (PPCG), integrating SBS, ID, CX and complex SV signatures. Eight footprints account for the processes in 85% of cases www.nature.com/articles/s41... @nature.com
🧵 We mapped the mutational processes shaping 959 prostate cancer genomes from the Pan Prostate Cancer Group (PPCG), integrating SBS, ID, CX and complex SV signatures. Eight footprints account for the processes in 85% of cases www.nature.com/articles/s41... @nature.com
Integrated signatures define mutational processes in prostate cancer - Nature
Eight integrated mutational footprints collectively explain the mutational processes in 85% of primary prostate cancer genomes.
www.nature.com
September 12, 2026 at 11:09 AM
Checkout our latest in @nature.com Integrated Mutational Footprints (SBS+Indels+SV+CIN signatures) define the mutational processes shaping 85% of prostate cancer genomes and outcomes. Explainer 👇
Extension to ska 'skalo' -- using local assembly to recover indels and MNPs where split k-mers mismatch
www.biorxiv.org/content/10.1...
We hope to integrate this into the main ska package in future too
www.biorxiv.org/content/10.1...
We hope to integrate this into the main ska package in future too
skalo: using SKA split k-mers with coloured de Brujin graphs to genotype indels
Insertions and deletions (indels) are important contributors to the genetic diversity and evolution of pathogens like Mycobacterium tuberculosis. However, accurately identifying them from genomic data...
www.biorxiv.org
October 4, 2024 at 1:44 PM
Extension to ska 'skalo' -- using local assembly to recover indels and MNPs where split k-mers mismatch
www.biorxiv.org/content/10.1...
We hope to integrate this into the main ska package in future too
www.biorxiv.org/content/10.1...
We hope to integrate this into the main ska package in future too
I'm super excited to share my recent work with @grocklin.bsky.social “Structural and energetic analysis of stabilizing indel mutations” biorxiv.org/content/10.1.... 1/8
Structural and energetic analysis of stabilizing indel mutations
Amino acid insertions and deletions (indels) are among the most common protein mutations and necessitate changes to a protein’s backbone geometry. Examining how indels affect protein folding stability...
biorxiv.org
January 10, 2025 at 6:36 AM
I'm super excited to share my recent work with @grocklin.bsky.social “Structural and energetic analysis of stabilizing indel mutations” biorxiv.org/content/10.1.... 1/8