Robert Kofler
@rokofler.bsky.social
📤 201
📥 130
📝 19
reposted by
Robert Kofler
Oded Rechavi
2 days ago
The idea is to decouple the journals from the review step. They’ll still exist, but they’ll need to add other value. They’ll highlight, curate, add new perspectives. If they do a good job they can still be prestigious (like Scientific American or Wired) (1.2) 👇
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reposted by
Robert Kofler
Luca Soldini
14 days ago
(1/9) Join us in Bern, Switzerland (8–11 Feb 2026) for our EMBO Workshop on Molecular Mechanisms of Selfish Elements and Strategies! Organized with Tanja Schwander, Laura Ross (
@laurarossevo.bsky.social
) and Axel Imhof.
meetings.embo.org/event/26-sel...
#EMBOselfishElements
#EMBOevents
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Molecular mechanisms of selfish elements and strategies
Certain genes, chromosomes, organelles, or entire sets of chromosomes can bias their transmission to the next generation, propagating themselves at the expense of the rest of the genome. Referred to …
https://meetings.embo.org/event/26-selfish-elements
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super cool - I am constantly wondering about the effects of recent TE invasions? lethal mutations seems to be one striking effect
www.biorxiv.org/content/10.1...
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Transposable elements drive much of naturally occurring genetic lethality in Drosophila melanogaster
Recessive lethal mutations are widespread across studied species, with estimates suggesting that each individual carries at least one. Numerous lethal alleles persist in wild populations at higher fre...
https://www.biorxiv.org/content/10.1101/2025.10.16.682755v1
19 days ago
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reposted by
Robert Kofler
DrosEU
22 days ago
We are in Bluesky and we are happy to share our two last consortium publications: the DrosEU expanded DEST dataset and a Continent-wide study of phenotypic differentiation among European
#Drosophila
melanogaster populations (1/7)
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reposted by
Robert Kofler
HEAS
28 days ago
@kuhlwilm.bsky.social
from
#HEASVienna
introducing
@rokofler.bsky.social
for the
#HEASSeminar
in
#AncientGenomics
taking place now online and in-person at the
#UBB
@univie.ac.at
add a skeleton here at some point
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reposted by
Robert Kofler
HEAS
about 1 month ago
We are looking forward to welcoming
@rokofler.bsky.social
to
#HEASVienna
as part of the
#HEASSeminar
in
#AncientGenomics
. Please note the slightly earlier start time of 10:00 CEST. More information and registration on our website 👇🔗
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HEAS Seminar Series - Ancient Genomics - HEAS
As part of the HEAS Seminar Series in Ancient Genomics, Robert Kofler from Vetmeduni Vienna will give a talk on Museomics reveals whether humans triggered widespread genome invasions across species on...
https://www.heas.at/events/heas-seminar-series-ancient-genomics-27/
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I'm wondering if this is not a unique, once in a lifetime opportunity, to study the spread and silencing of an iERV in a natural population. last time we checked it was not yet in Vienna
add a skeleton here at some point
about 1 month ago
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reposted by
Robert Kofler
Darren Obbard
about 2 months ago
Another preprint from
@pankajd.bsky.social
!
www.biorxiv.org/content/10.1...
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Predictors of protein evolution in the drosophilid immune system
The evolutionary dynamics of immune genes are shaped by diverse selective pressures, yet the relative roles of gene-level traits, functional specialization, and pathway context remain poorly understoo...
https://www.biorxiv.org/content/10.1101/2025.09.11.675540v1
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reposted by
Robert Kofler
Yun S. Song
2 months ago
SINGER, our ARG inference method, is finally published and freely available online:
doi.org/10.1038/s415...
It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
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Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics
SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.
https://doi.org/10.1038/s41588-025-02317-9
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reposted by
Robert Kofler
Justin Blumenstiel
2 months ago
In all my obsession with RNA silencing, I realized I became blind to the significance of autoregulation of DNA transposons. Which is funny, because it was characterized in many ways by my Ph.D. advisor. From 2013:
elifesciences.org/articles/00668
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The autoregulation of a eukaryotic DNA transposon
A DNA transposon, or ‘jumping gene’, controls its amplification within a genome through a competition between the enzyme multimers that are responsible for its mobility.
https://elifesciences.org/articles/00668
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reposted by
Robert Kofler
Amelia Cervera 🍉
2 months ago
#TEsky
add a skeleton here at some point
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reposted by
Robert Kofler
Matt Beaumont
2 months ago
Germline defence from TEs largely relies on piRNAs. Yet,
@divyaselvaraju.bsky.social
and I monitored a P-element invasion in Drosophila that was stopped by an internally deleted copy, no host intervention required!
doi.org/10.1371/jour...
Many thanks to
@rpianezza.bsky.social
&
@rokofler.bsky.social
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Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence
Author summary Transposable elements (TEs) are short, self-replicating DNA sequences found in nearly all genomes. While they can be harmful to their hosts, many organisms have evolved defence systems,...
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011649
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reposted by
Robert Kofler
Dr. Sarah Signor
3 months ago
@shashankpritam.bsky.social
first research paper on the effect of insertion bias on transposon fitness!! With
@almoroscarpa.bsky.social
and
@rokofler.bsky.social
link.springer.com/article/10.1...
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The impact of insertion bias into piRNA clusters on the invasion of transposable elements - BMC Biology
Background In our current understanding of transposable element (TE) invasions, TEs move freely until they accidentally insert into a piRNA cluster, where they are silenced by the production of piRNA ...
https://link.springer.com/article/10.1186/s12915-025-02370-0?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20250815&utm_content=10.1186%2Fs12915-025-02370-0
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reposted by
Robert Kofler
Julius Brennecke
3 months ago
piRNAs are essential for transposon silencing in the animal germline. But how do hosts trap transposon sequences in genomic loci that help establish a piRNA response? Looking at a natural transposon invasion, Baptiste Rafanel and Kirsten Senti made some remarkable observations.
add a skeleton here at some point
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reposted by
Robert Kofler
Clément Goubert
4 months ago
Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties
www.biorxiv.org/content/10.1...
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Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties
Transposable elements are genetic parasites whose mobilization throughout the genome is a major source of deleterious mutations. However, some TE insertions are beneficial because they improve host fi...
https://www.biorxiv.org/content/10.1101/2025.07.17.665384
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reposted by
Robert Kofler
Julius Brennecke
4 months ago
@rokofler.bsky.social
uncovered a treasure cove in Drosophila populations here. Remarkable and highly relevant findings on horizontal transfer of all kinds of TEs, irrespective of their transposition type.
add a skeleton here at some point
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reposted by
Robert Kofler
4 months ago
@rokofler.bsky.social
talks about the spread of TEs in drosophila over time - are humans responsible??
#smbe2025
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reposted by
Robert Kofler
Molecular Biology and Evolution
4 months ago
@rpianezza.bsky.social
@almoroscarpa.bsky.social
, A. Haidar,
@signor-molevol.bsky.social
&
@rokofler.bsky.social
investigated 11 TEs in D. melanogaster that added ~1 Mbp via horizontal transfer, likely from other Drosophila spp. 🔗
doi.org/10.1093/molbev/msaf143
#evobio
#drosophila
#TEsky
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Spatiotemporal Tracking of Three Novel Transposable Element Invasions in Drosophila melanogaster over the Last 30 Years
Abstract. Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a significant influence on evolution througho
https://doi.org/10.1093/molbev/msaf143
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reposted by
Robert Kofler
Society for Molecular Biology and Evolution
4 months ago
Talks by:
@gonzalezlabbcn.bsky.social
Yalong Guo Axel Meyer Emmanuelle Lerat Cheng Sun Qiheng Xu Jie Cui Ilia Kirov Chengyi Song Li Wang Jing Wang
@rokofler.bsky.social
Ying Liu Shengjun Tan
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super-happy, three TE invasions in Dmel during the last 30 years; the crazy thing - Transib1 spread in just 2-3years in global populations
academic.oup.com/mbe/advance-...
great work everyone
@rpianezza.bsky.social
@almoroscarpa.bsky.social
@signor-molevol.bsky.social
Anna Haider
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Spatio-temporal tracking of three novel transposable element invasions in Drosophila melanogaster over the last 30 years
Abstract. Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a sigfinificant influence on evolution throug
https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaf143/8157961
5 months ago
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reposted by
Robert Kofler
Dr. Sarah Signor
5 months ago
The work on TE invasions in D. melanogaster continues! We found three more recent invasions, one of which occurred in ~3 years worldwide. Another great collaboration with
@rpianezza.bsky.social
@rokofler.bsky.social
and others
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https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaf143/8157961
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reposted by
Robert Kofler
Dmitri Petrov
5 months ago
Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did!
www.philanthropy.cam.ac.uk/give-to-camb...
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Drosophila Genetic Database
The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...
https://www.philanthropy.cam.ac.uk/give-to-cambridge/physiology-development-and-neuroscience/drosophila-genetic-database
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great work of Riccardo tracing the origin of D.melanogaster transposons
add a skeleton here at some point
5 months ago
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this is fantastic news - congrats Philipp :)
add a skeleton here at some point
6 months ago
0
1
0
reposted by
Robert Kofler
PopGen Vienna
7 months ago
Our
#PhD
student Almorò Scarpa
@almoroscarpa.bsky.social
looks forward to
#PopGen
meeting tomorrow! He will tell us about "Two centuries of transposable element invasions in Drosophila melanogaster" Full schedule and streaming details at
www.popgen-vienna.at/news/seminars/
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Seminars
https://www.popgen-vienna.at/news/seminars/
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Super proud of amazing PhD student Sarah Saadain winning the Carl von Schreibers prize with her cockroach project; Vetmeduni Wien and
@nhmwien.bsky.social
www.nhm-wien.ac.at/presse/press...
8 months ago
0
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1
reposted by
Robert Kofler
Clément Goubert
8 months ago
Polymorphic transposable elements contribute to variation in recombination landscapes (drosohila 🪰)
www.pnas.org/doi/full/10....
#TEsky
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PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
https://www.pnas.org/doi/full/10.1073/pnas.2427312122
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reposted by
Robert Kofler
Maya Voichek
8 months ago
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
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reposted by
Robert Kofler
Oded Rechavi
8 months ago
The truth is that the scientific process is horribly inefficient and wasteful. But the solution is NOT cutting funds and it’s NOT top down guidance of what should be studied. Instead, we should revolutionize how we publish and improve peer review.
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reposted by
Robert Kofler
Cedric Feschotte
8 months ago
Did you know that some bacteria have linear chromosomes? Not only that, but as in certain eukaryotes (most famously 🪰) bacterial telomeres can be capped by specialized transposons!! Exciting 🤯 work by fellow transposon lovers in the Peters lab @ Cornell - congrats to all!
add a skeleton here at some point
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reposted by
Robert Kofler
Cedric Feschotte
8 months ago
Viva Vienna!
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reposted by
Robert Kofler
Trends in Genetics
9 months ago
In this new Feature Review, Yukihide Tomari and colleagues examine repression mechanisms that silence transposons and discuss the dynamic coevolution of transposons and host defenses in animals. Read for FREE till April 11th:
authors.elsevier.com/a/1keCScQbJF...
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Our new paper on the P-element invasion in D.simulans
mobilednajournal.biomedcentral.com/articles/10....
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On the origin of the P-element invasion in Drosophila simulans - Mobile DNA
The horizontal transfer (HT) of the P-element is one of the best documented cases of the HT of a transposable element. The P-element invaded natural D. melanogaster populations between 1950 and 1980 f...
https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-025-00345-0
9 months ago
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reposted by
Robert Kofler
Vega Shah
9 months ago
me and my folder of papers i downloaded to read later
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reposted by
Robert Kofler
Cedric Feschotte
9 months ago
Feels awkward but necessary to celebrate scientific progress in this imperiled time for US biomedical research. Proud of our latest paper out today exploring the role of transposable elements in antiviral resistance to HIV 🦠
genomebiology.biomedcentral.com/articles/10....
🧵1/n
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Transposable elements may enhance antiviral resistance in HIV-1 elite controllers - Genome Biology
Background Less than 0.5% of people living with HIV-1 are elite controllers (ECs)—individuals who maintain undetectable plasma viremia without antiretroviral therapy, despite having replication-compet...
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03484-y
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reposted by
Robert Kofler
Clément Goubert
9 months ago
Very promising approach to characterize the mobilome in pangenomes from ! I wonder how this compares/complements to Pantera (
@piosierra.bsky.social
) and GraffiTE
www.biorxiv.org/content/10.1...
#TESky
#SV
#Pangenomes
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Pannagram: unbiased pangenome alignment and the Mobilome calling
Pannagram is a toolkit for unbiased pangenome alignment and Mobilome detection based on full-genome assemblies. It consists of two components: a command-line interface for performing the multiple geno...
https://www.biorxiv.org/content/10.1101/2025.02.07.637071v1
0
10
2
reposted by
Robert Kofler
Daniel Croll
10 months ago
@tbadet.bsky.social
and I have a preprint out on transposon silencing in fungi! Genome size evolution is fascinating and showcases the dynamic nature of transposon activation. What we understand less are the dynamics of transposon defense systems encoded by the genomes.
doi.org/10.1101/2025...
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reposted by
Robert Kofler
Casey Bergman
10 months ago
New Bergman Lab paper now online at GBE: "Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces"
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Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces
Abstract. Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history an
https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evaf004/7950627?login=false
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reposted by
Robert Kofler
Dr. Sarah Signor
10 months ago
This collaboration was such a pleasure. Our new paper on cascades of HT after introduction of two TEs to human commensals
www.nature.com/articles/s41...
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Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years - Nature Communications
Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, the authors show that two transposable elements, Shellder and Spoink, invaded...
https://www.nature.com/articles/s41467-024-55779-6?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20250109&utm_content=10.1038/s41467-024-55779-6
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reposted by
Robert Kofler
Cedric Feschotte
10 months ago
It’s often assumed that the horizontal transfer of transposons btw animals is rare (Myr scale). But recent detective work by Kofler lab & others suggest HT must be very frequent, so that a single transposon can successfully invade multiple species around the world in just a few decades! Wild!
add a skeleton here at some point
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super proud - our new work about the invasions triggered by two troublesome TEs in Nat. Comm.
www.nature.com/articles/s41...
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Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years - Nature Communications
Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, the authors show that two transposable elements, Shellder and Spoink, invaded...
https://www.nature.com/articles/s41467-024-55779-6?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20250109&utm_content=10.1038/s41467-024-55779-6
10 months ago
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reposted by
Robert Kofler
PlantEvolution 🌱🌾
11 months ago
Announcing a curated collection of long-read genomes for Arabidopsis thaliana: The 1001 Genomes Plus Project. Currently 453 unique accessions/almost 600 assemblies. Interested in contributing? Please contact us!
#plantscience
www.biorxiv.org/content/10.1...
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reposted by
Robert Kofler
phy_papers
11 months ago
Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
http://biorxiv.org/cgi/content/short/2024.12.18.629015v1
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Good news: Deadline exend for Genome Biology collection on transposable elements in genome evolution: March 21.
www.biomedcentral.com/collections/...
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Call for papers - Transposable elements in genome evolution
https://www.biomedcentral.com/collections/TEGE
11 months ago
0
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Our novel tool for finding recent TE invasions without repeat library - great work by amazing student Riccardo (not yet on bsky)
genomebiology.biomedcentral.com/articles/10....
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GenomeDelta: detecting recent transposable element invasions without repeat library - Genome Biology
We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-qualit...
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03459-5
11 months ago
0
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reposted by
Robert Kofler
The Interactive Fly
11 months ago
Pianezza, R., Scarpa, A., Narayanan, P., Signor, S., Kofler, R. (2024). Spoink, a LTR retrotransposon, invaded
#Drosophila
melanogaster populations in the 1990s. PLoS Genet, 20(3):e1011201
journals.plos.org/plosgenetics...
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Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s
Author summary Horizontal transfer of transposable elements (TE) is a major factor driving genome evolution. Yet well documented cases of such horizontal transfer events are rare. Most evidence is ind...
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011201
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reposted by
Robert Kofler
Dr. Sarah Signor
11 months ago
My graduate student shashank and I wrote this cool review on the evolution of transposon defense. Come for pirna cluster evolution stay for wild theories!
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Evolution of piRNA-guided defense against transposable elements
Transposable elements (TEs) shape every aspect of genome biology, influencing genome stability, size, and organismal fitness. Following the 2007 disco…
https://www.sciencedirect.com/science/article/pii/S0168952524002932?dgcid=author
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reposted by
Robert Kofler
David L. Stern
11 months ago
Want to perform HIGH EFFICIENCY Homology Directed Repair in Drosophila spp? Try Atalanta plasmids. About 10X higher efficiency than other methods! Tag or delete genes, invert chromosome regions, make scarless site-specific modifications. All with easy cloning. This paper is proudly bioRxiv only!
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reposted by
Robert Kofler
Etienne Bucher 🌾🧬🇪🇺
12 months ago
Interesting findings about one of my favorite Transposons called ÉVADÉ: PTGS is dispensable for the initiation of epigenetic silencing of an active transposon in Arabidopsis.
www.embopress.org/doi/full/10....
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reposted by
Robert Kofler
Dmitri Petrov
12 months ago
Very proud to be a part of this incredible effort! "Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource"
www.biorxiv.org/content/10.1...
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Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource
Large scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster , we p...
https://www.biorxiv.org/content/10.1101/2024.11.10.622744v1
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