Lars Podsiadlowski
@lpodsiadlowski.bsky.social
Scientific lab head at a natural history museum (LIB / Museum König Bonn, Germany). Research in animal genomics & evolution (insects, fish), teaching bioinformatics. Enjoying literature & history, 50/60s Jazz and arthouse movies.
Reposted by Lars Podsiadlowski
Really excited that our DFG grant on the Speciation Genomics of Eye Size variation in *Heliconius* has been funded :) In the next weeks, I will post an advert for a PhD, but if you know of good students, please suggest they get in touch. Please repost.
April 22, 2025 at 7:28 AM
Really excited that our DFG grant on the Speciation Genomics of Eye Size variation in *Heliconius* has been funded :) In the next weeks, I will post an advert for a PhD, but if you know of good students, please suggest they get in touch. Please repost.
Reposted by Lars Podsiadlowski
#ERGAReads | Thinking of sequencing a genome in your lab? 🧬 This review offers practical guidance on how to start a #genome project for non-model species - covering DNA extraction, sequencing tech, costs, and more!
🔗 rdcu.be/eiHRG
@sgn.one @leibnizlib.bsky.social #biodiversity #genomics
🔗 rdcu.be/eiHRG
@sgn.one @leibnizlib.bsky.social #biodiversity #genomics
April 23, 2025 at 8:11 AM
#ERGAReads | Thinking of sequencing a genome in your lab? 🧬 This review offers practical guidance on how to start a #genome project for non-model species - covering DNA extraction, sequencing tech, costs, and more!
🔗 rdcu.be/eiHRG
@sgn.one @leibnizlib.bsky.social #biodiversity #genomics
🔗 rdcu.be/eiHRG
@sgn.one @leibnizlib.bsky.social #biodiversity #genomics
Reposted by Lars Podsiadlowski
Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...
Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species
The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genome...
www.biorxiv.org
April 21, 2025 at 5:37 AM
Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...
Reposted by Lars Podsiadlowski
Here we describe the motivations and methods behind our #A3Cat resource - Arthropoda Assembly Assessment Catalogue (website here: a3cat.unil.ch) academic.oup.com/gigascience/... currently with 7'321 #arthropod #genome assemblies
Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes
AbstractBackground. Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rap
academic.oup.com
April 20, 2025 at 12:05 PM
Here we describe the motivations and methods behind our #A3Cat resource - Arthropoda Assembly Assessment Catalogue (website here: a3cat.unil.ch) academic.oup.com/gigascience/... currently with 7'321 #arthropod #genome assemblies
Reposted by Lars Podsiadlowski
Do you use Darwin Tree of Life (DToL) genomes for your work or grant applications? If so, can you please fill out this form? docs.google.com/forms/d/e/1F... We are gathering info on how DToL genomes are used. It will help us raise money to continue producing publicly available high-quality genomes.
Darwin Tree of Life Impact Assessment
This form is used to share information within DToL about case studies, ongoing research, and funding awards that demonstrate the impact the Darwin Tree of Life consortium project has had on Global and...
docs.google.com
February 24, 2025 at 8:29 PM
Do you use Darwin Tree of Life (DToL) genomes for your work or grant applications? If so, can you please fill out this form? docs.google.com/forms/d/e/1F... We are gathering info on how DToL genomes are used. It will help us raise money to continue producing publicly available high-quality genomes.
Reposted by Lars Podsiadlowski
if you are trying to get HMW DNA out of any species, have a look at the stellar progress from Sanger Tree of Life core lab who have now extracted DNA from 1000s of species. Paper showcasing things learned along the way now up on bioRxiv at www.biorxiv.org/content/10.1...
April 14, 2025 at 1:25 PM
if you are trying to get HMW DNA out of any species, have a look at the stellar progress from Sanger Tree of Life core lab who have now extracted DNA from 1000s of species. Paper showcasing things learned along the way now up on bioRxiv at www.biorxiv.org/content/10.1...
Reposted by Lars Podsiadlowski
tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets. #TelomericRepeats #AssembledGenomces #LongReads #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets
AbstractSummary. tidk (short for telomere identification toolkit), uses a simple, fast algorithm to scan long DNA reads for the presence of short tandemly
academic.oup.com
February 10, 2025 at 10:18 PM
tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets. #TelomericRepeats #AssembledGenomces #LongReads #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Lars Podsiadlowski
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads https://www.biorxiv.org/content/10.1101/2025.04.14.648685v1
April 18, 2025 at 3:46 AM
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads https://www.biorxiv.org/content/10.1101/2025.04.14.648685v1
Reposted by Lars Podsiadlowski
To support genome structure studies in non-model systems, we developed SyntenyFinder, a synteny analysis pipeline combining OrthoFinder and RIdeogram. Learn more on our GitHub: github.com/symgenoevola...
GitHub - symgenoevolab/SyntenyFinder: SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-lev...
SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI. - s...
github.com
January 7, 2025 at 6:20 AM
To support genome structure studies in non-model systems, we developed SyntenyFinder, a synteny analysis pipeline combining OrthoFinder and RIdeogram. Learn more on our GitHub: github.com/symgenoevola...
Reposted by Lars Podsiadlowski
De novo genes research community 🧬 - please consider using for your future or past work our new methodology annotation format for better comparability of studies and higher reproducibility. (1/3)
DeNoFo: a file format and toolkit for standardised, comparable de novo gene annotation https://www.biorxiv.org/content/10.1101/2025.03.31.644673v1
April 3, 2025 at 3:04 PM
De novo genes research community 🧬 - please consider using for your future or past work our new methodology annotation format for better comparability of studies and higher reproducibility. (1/3)
Reposted by Lars Podsiadlowski
Still no reading material for the Easter break🌞🌻🐰? Then I have a suggestion: "Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide" (lnkd.in/dsRmSBDE). It was a pleasure to work on this new publication with TilmanSchell & @lpodsiadlowski.bsky.social🙏!
April 17, 2025 at 10:40 AM
Still no reading material for the Easter break🌞🌻🐰? Then I have a suggestion: "Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide" (lnkd.in/dsRmSBDE). It was a pleasure to work on this new publication with TilmanSchell & @lpodsiadlowski.bsky.social🙏!
Reposted by Lars Podsiadlowski
Gonna write a paper on this. PLEASE DON'T USE VCFTOOLS TO CALCULATE π. It is a random number generator, as the software assumes all bp that aren't SNPs are invariant (i.e. ignores missing data). This is especially bad in plant genomes, with abundant TEs where you can't map reads.
February 1, 2024 at 5:19 PM
Gonna write a paper on this. PLEASE DON'T USE VCFTOOLS TO CALCULATE π. It is a random number generator, as the software assumes all bp that aren't SNPs are invariant (i.e. ignores missing data). This is especially bad in plant genomes, with abundant TEs where you can't map reads.
Reposted by Lars Podsiadlowski
You need to use PIXY with a gvcf, ANGSD with genotype likelihoods, or MOP to estimate the number of bp with data in each window to use as a denominator.
pixy.readthedocs.io
www.popgen.dk/angsd/index....
github.com/RILAB/mop
pixy.readthedocs.io
www.popgen.dk/angsd/index....
github.com/RILAB/mop
GitHub - RILAB/mop: Simple tool for capturing alignment regions with sufficient quality for genotypi...
Simple tool for capturing alignment regions with sufficient quality for genotyping. - GitHub - RILAB/mop: Simple tool for capturing alignment regions with sufficient quality for genotyping.
github.com
February 1, 2024 at 5:20 PM
You need to use PIXY with a gvcf, ANGSD with genotype likelihoods, or MOP to estimate the number of bp with data in each window to use as a denominator.
pixy.readthedocs.io
www.popgen.dk/angsd/index....
github.com/RILAB/mop
pixy.readthedocs.io
www.popgen.dk/angsd/index....
github.com/RILAB/mop
Transmissible cancer in marine mussels. On depth study this week on the cover of @NatureCancer
Nature Cancer - Transmissible marine cancer evolution
Transmissible leukemia-like cancer in the marine species Cerastoderma edule and Mya arenaria is characterized by long-term tolerance as well as genomic...
www.nature.com
November 28, 2023 at 8:26 AM
Transmissible cancer in marine mussels. On depth study this week on the cover of @NatureCancer
Reposted by Lars Podsiadlowski
Discover what it's like to be a #bee from author Lars Chittka in today's Ideas post.
press.princeton.edu/ideas/what-i...
#Science #Nature #bees #AnimalBehavior
press.princeton.edu/ideas/what-i...
#Science #Nature #bees #AnimalBehavior
November 27, 2023 at 8:42 PM
Discover what it's like to be a #bee from author Lars Chittka in today's Ideas post.
press.princeton.edu/ideas/what-i...
#Science #Nature #bees #AnimalBehavior
press.princeton.edu/ideas/what-i...
#Science #Nature #bees #AnimalBehavior
Reposted by Lars Podsiadlowski
Horizontally transferred cell-free chromatin particles function as miniature predatory genomes and vehicles for transposable elements within host cells https://www.biorxiv.org/content/10.1101/2023.11.21.567988v1
Horizontally transferred cell-free chromatin particles function as miniature predatory genomes and vehicles for transposable elements within host cells https://www.biorxiv.org/content/10.1101/2023.11.21.567988v1
Background: Horizontal gene transfer is known to drive adaptation and evolutionary processes in micr
www.biorxiv.org
November 22, 2023 at 1:39 AM
Horizontally transferred cell-free chromatin particles function as miniature predatory genomes and vehicles for transposable elements within host cells https://www.biorxiv.org/content/10.1101/2023.11.21.567988v1
Reposted by Lars Podsiadlowski
Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads https://www.biorxiv.org/content/10.1101/2023.11.21.568046v1
Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads https://www.biorxiv.org/content/10.1101/2023.11.21.568046v1
Mapping transcriptomic variations using either short or long reads RNA sequencing is a staple of gen
www.biorxiv.org
November 22, 2023 at 3:53 AM
Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads https://www.biorxiv.org/content/10.1101/2023.11.21.568046v1
Reposted by Lars Podsiadlowski
Reposted by Lars Podsiadlowski
A large-scale assessment of sequence database search tools for homology-based protein function prediction https://www.biorxiv.org/content/10.1101/2023.11.14.567021v1
A large-scale assessment of sequence database search tools for homology-based protein function prediction https://www.biorxiv.org/content/10.1101/2023.11.14.567021v1
Sequence database searches followed by homology-based function transfer form one of the oldest and m
www.biorxiv.org
November 17, 2023 at 2:53 AM
A large-scale assessment of sequence database search tools for homology-based protein function prediction https://www.biorxiv.org/content/10.1101/2023.11.14.567021v1
Reposted by Lars Podsiadlowski
In my latest newsletter, I'm excited to announce my 3rd book!
THE INFINITE EXTENT. A book about life at different scales--of size, time, geography, longevity, connectivity, individuality, & more.
I see it as the conclusion of a trilogy of books.
More details: buttondown.email/edyong209/ar...
THE INFINITE EXTENT. A book about life at different scales--of size, time, geography, longevity, connectivity, individuality, & more.
I see it as the conclusion of a trilogy of books.
More details: buttondown.email/edyong209/ar...
November 15, 2023 at 10:09 PM
In my latest newsletter, I'm excited to announce my 3rd book!
THE INFINITE EXTENT. A book about life at different scales--of size, time, geography, longevity, connectivity, individuality, & more.
I see it as the conclusion of a trilogy of books.
More details: buttondown.email/edyong209/ar...
THE INFINITE EXTENT. A book about life at different scales--of size, time, geography, longevity, connectivity, individuality, & more.
I see it as the conclusion of a trilogy of books.
More details: buttondown.email/edyong209/ar...
Reposted by Lars Podsiadlowski
The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education onlinelibrary.wiley.com/doi/10.1002/...
November 13, 2023 at 7:11 AM
The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Lars Podsiadlowski
A major change in the BRAKER genome annotation world: The GeneMark-Team changed the license of GeneMark (thank you so much!!!). There is no more need to install a license key file. Also GeneMark-ETP has improved stability due to their efforts. github.com/Gaius-August...
November 7, 2023 at 2:18 PM
A major change in the BRAKER genome annotation world: The GeneMark-Team changed the license of GeneMark (thank you so much!!!). There is no more need to install a license key file. Also GeneMark-ETP has improved stability due to their efforts. github.com/Gaius-August...
Reposted by Lars Podsiadlowski
Call for Papers! Genome Research is now encouraging submissions for a Special Issue on Long-read DNA Sequencing Applications in Biology and Medicine, Guest Edited by Ana Conesa, Alexander Hoischen, and Fritz Sedlazeck @sedlazeck.bsky.social. bit.ly/grcallforpapers #longreads #T2T #ASHG23
November 19, 2024 at 10:30 PM
Call for Papers! Genome Research is now encouraging submissions for a Special Issue on Long-read DNA Sequencing Applications in Biology and Medicine, Guest Edited by Ana Conesa, Alexander Hoischen, and Fritz Sedlazeck @sedlazeck.bsky.social. bit.ly/grcallforpapers #longreads #T2T #ASHG23
Reposted by Lars Podsiadlowski
Today we publish a new paper on a molecular phylogeny of true crabs. We find crabs transitioned from marine to non-marine environments 7-17x over 100+ myr! This culminates 15+ years(!) of effort from an international team! 1/4 (thread in replies)
academic.oup.com/sysbio/advan...
🧪🦀🦑#evosky
academic.oup.com/sysbio/advan...
🧪🦀🦑#evosky
November 6, 2023 at 4:18 PM
Today we publish a new paper on a molecular phylogeny of true crabs. We find crabs transitioned from marine to non-marine environments 7-17x over 100+ myr! This culminates 15+ years(!) of effort from an international team! 1/4 (thread in replies)
academic.oup.com/sysbio/advan...
🧪🦀🦑#evosky
academic.oup.com/sysbio/advan...
🧪🦀🦑#evosky