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Wenfei Xian (冼文飞)

@wenfeixian.bsky.social
107 followers 156 following 7 posts

PhD student in Weigel world www.weigelworld.org how genetic variants are generated, how they evolve, and how they are maintained in the genomes. github: github.com/Wenfei-Xian

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Reposted by Wenfei Xian (冼文飞)
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 02/08/2025
1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab. Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes. #plantscience www.biorxiv.org/content/10.1...
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Wenfei Xian (冼文飞) @wenfeixian.bsky.social · 07/08/2025
😃
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Wenfei Xian (冼文飞) @wenfeixian.bsky.social · 06/08/2025
Super happy to share that I’ve passed my PhD defense! 🍾 It’s been an amazing journey doing my PhD in the Weigel World. Huge thanks to my supervisor, Detlef @plantevolution.bsky.social , even with your crazy schedule, you always made time to guide me. Couldn’t have done it without all your support!!!
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Reposted by Wenfei Xian (冼文飞)
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 10/02/2025
In our latest @biorxiv-genomic.bsky.social preprint, we describe our approach to use PacBio HiFi reads to detect somatic TE transposition -- good enough to detect rare events that are present in only single cells. Led by Andrea Movilli. #plantscience www.biorxiv.org/content/10.1...
Diagram of somatic TE insertions across the A. thaliana genome
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Wenfei Xian (冼文飞) @wenfeixian.bsky.social · 15/01/2025
Large repeats are common in plant organellar genomes. Half of the A. thaliana mitogenomes we assembled have two large repeat pairs, while others have only one, where we identified two potential HGT events. Large repeats link to geography and cold traits. Feedback welcome on bioRxiv, Email, etc.!
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Reposted by Wenfei Xian (冼文飞)
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 27/12/2024
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 Wenfei Xian (冼文飞)
Houming Chen @hmchen93.bsky.social · 17/11/2024
Super excited to announce that our SCRM story is officially published!!! 🎉🎉🎉 Want to discover the exciting new functions of ICE1/SCRM? Want to dive into the latest model of plant embryo initiation? Don’t miss out—check it out here: nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com
Phosphorylation‐dependent activation of the bHLH transcription factor ICE1/SCRM promotes polarization of the Arabidopsis zygote
In Arabidopsis thaliana, the asymmetric cell division (ACD) of the zygote gives rise to the embryo proper and an extraembryonic suspensor, respectively. This process is controlled by the ERECTA-YODA...
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 07/04/2024
Accessory proteins increase the efficiency of RNA editing by Arabidopsis chloroplast editosomes www.biorxiv.org/content/10.1101/202…
biorxiv.org
Accessory proteins increase the efficiency of RNA editing by Arabidopsis chloroplast editosomes https://www.biorxiv.org/content/10.1101/2024.04.05.588343v1
RNA editing modifies cytidines to uridines in plant organelle transcripts so that their sequence dif
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 07/04/2024
Effects of spontaneous mutations on survival and reproduction of Drosophila serrata infected with Drosophila C virus www.biorxiv.org/content/10.1101/202…
biorxiv.org
Effects of spontaneous mutations on survival and reproduction of Drosophila serrata infected with Drosophila C virus https://www.biorxiv.org/content/10.1101/2024.04.04.588202v1
The impact of selection on host immune function genes has been widely documented. However, it remain
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Reposted by Wenfei Xian (冼文飞)
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 04/04/2024
How cool is that -- would not have guessed that the type of genetic incompatibility, hybrid necrosis, that we've studied for many years, is also the cause for graft incompatibility. I wonder whether it's a story of mismatched helper NLRs... @kamounlab.bsky.social
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 30/03/2024
Transposable elements as evolutionary driving force to ecological speciation in cactophilic Drosophila species www.biorxiv.org/content/10.1101/202…
biorxiv.org
Transposable elements as evolutionary driving force to ecological speciation in cactophilic Drosophila species https://www.biorxiv.org/content/10.1101/2024.03.27.587021v1
Background The host shift in insects has been considered a key process with potential to collaborate
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Reposted by Wenfei Xian (冼文飞)
Leo C. Stein @duetosymmetry.com · 27/03/2024
The Event Horizon Telescope has measured the *polarized* radiation from our friendly neighborhood black hole, Sgr A*! Press release: eventhorizontelescope.org/blog/astrono..., papers in next skeet 🔭🧪
A view of the Milky Way supermassive black hole Sagittarius A* in polarized light.
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Reposted by Wenfei Xian (冼文飞)
Mario Coiro @lepidodendron.bsky.social · 22/03/2024
last week my latest paper on #cycads came out. The article deals with the idea of cycads as "living #fossils", but what does this mean exactly, and what did we actually test? A thread for #FossilFriday! www.nature.com/articles/s42...
nature.com
Disparity of cycad leaves dispels the living fossil metaphor - Communications Biology
An analysis of leaf disparity through time in cycads shows that this group has a dynamic and expanding morphological diversity until the present, and thus does not fit the ‘living fossil’ hypothesis o...
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Reposted by Wenfei Xian (冼文飞)
Space Telescope Science Institute @stsci.edu · 22/03/2024
Asymmetry has never been so pleasing! Hubble’s near-infrared and visible-light view shows jostled dark brown dust lanes and a core knocked off center. Why? Galaxy M96 is part of a group of galaxies in a gravitational “tug of war.” Credit: ESA/Hubble, NASA, and the LEGUS Team. 🔭 🧪
A spiral galaxy takes up almost the entire frame, from bottom left to top right. The circular-shaped galaxy is not seen perfectly face-on, but is slightly tilted. The galaxy has a bright light yellow central core that is surrounded by tightly wound spiral arms that are oriented counter clockwise. Beginning at the core and going to the right and then to the top are prominent, dark brown dust lanes. The other region forms an arc toward the bottom left, starting near the core at around 9 o’clock. The outer edges of the galaxy are where there are brighter blue areas filled with clusters of stars. Pink star clusters are found throughout, are most obvious toward the edges, and appear more clustered toward the middle-right edge and toward the bottom left corner. The background of space is black.
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 20/03/2024
Permutation analysis prior to variable selection greatly enhances robustness of OPLS analysis in small cohorts www.biorxiv.org/content/10.1101/202…
biorxiv.org
Permutation analysis prior to variable selection greatly enhances robustness of OPLS analysis in small cohorts https://www.biorxiv.org/content/10.1101/2024.03.18.585475v1
The R-workflow roplspvs (R orthogonal projections of latent structures with permutation over variabl
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Reposted by Wenfei Xian (冼文飞)
George Matsumoto @georgeimatsumoto.bsky.social · 16/03/2024
reposting to 🧪 cause it's a very cool paper
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 19/03/2024
IDRWalker: A Random Walk based Modeling Tool for Disordered Regions in Proteins www.biorxiv.org/content/10.1101/202…
biorxiv.org
IDRWalker: A Random Walk based Modeling Tool for Disordered Regions in Proteins https://www.biorxiv.org/content/10.1101/2024.03.17.585378v1
Motivation: With the advancement of structural biology techniques, the elucidation of increasingly l
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 18/03/2024
Estimation of spatial demographic maps from polymorphism data using a neural network www.biorxiv.org/content/10.1101/202…
biorxiv.org
Estimation of spatial demographic maps from polymorphism data using a neural network https://www.biorxiv.org/content/10.1101/2024.03.15.585300v1
A fundamental goal in population genetics is to understand how variation is arrayed over natural lan
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Reposted by Wenfei Xian (冼文飞)
Zhigui Bao 鲍志贵 @zbao.bsky.social · 17/03/2024
T2T with ONT-only 🏃🏻🍅🌽
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 17/03/2024
Characterising tandem repeat complexities across long-read sequencing platforms with TREAT www.biorxiv.org/content/10.1101/202…
biorxiv.org
Characterising tandem repeat complexities across long-read sequencing platforms with TREAT https://www.biorxiv.org/content/10.1101/2024.03.15.585288v1
Tandem repeats (TR) play important roles in genomic variation and disease risk in humans. Long-read
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Reposted by Wenfei Xian (冼文飞)
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 16/03/2024
German-Spanish-Argentinean collaboration on haplotype-resolved Malbec 🍇🍷genome. Trio-binning used short reads from the parental varietals Prunelard and Magdeleine Noire des Charentes, which are both almost extinct academic.oup.com/hr/advance-a...
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 16/03/2024
Global climate change effect on Asian Mus musculus; Implication from last glacial maximum to the end of the 21st century www.biorxiv.org/content/10.1101/202…
biorxiv.org
Global climate change effect on Asian Mus musculus; Implication from last glacial maximum to the end of the 21st century https://www.biorxiv.org/content/10.1101/2024.03.14.584992v1
Global climate change poses unprecedented challenges to biodiversity, prompting urgent investigation
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 16/03/2024
FST and genetic diversity in an island model with background selection www.biorxiv.org/content/10.1101/202…
biorxiv.org
FST and genetic diversity in an island model with background selection https://www.biorxiv.org/content/10.1101/2024.03.15.585154v1
Background selection, by which selection on deleterious alleles reduces diversity at linked neutral
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 15/03/2024
Genome streamlining: effect of mutation rate and population size on genome size reduction www.biorxiv.org/content/10.1101/202…
biorxiv.org
Genome streamlining: effect of mutation rate and population size on genome size reduction https://www.biorxiv.org/content/10.1101/2024.03.14.584996v1
Genome streamlining, i.e. genome size reduction, is observed in bacteria with very different life tr
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Reposted by Wenfei Xian (冼文飞)
Space Telescope Science Institute @stsci.edu · 14/03/2024
The #Hubble images used in this animated science visualization present a full rotation of #Jupiter. It's not a real-time movie, but snapshots of the planet, taken in January, have been photo-mapped onto a sphere, and the model is then rotated in animation. 🔭 🧪
youtu.be
Jupiter Rotation using the Hubble Space Telescope - 2024
The Hubble Space Telescope images used in this animated science visualization present a full rotation of the giant planet Jupiter. This is not a real-time mo...
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Reposted by Wenfei Xian (冼文飞)
Sophien Kamoun @kamounlab.bsky.social · 13/03/2024
#Fungal24 gone the sorry way of Gordon Conference with overly restrictive policy on social media, posters etc. pretty bad given the conference is way oversubscribed. ECRs, why don’t you publish your posters instead? kamounlab.medium.com/why-you-shou...
kamounlab.medium.com
Why you should publish your posters
Publishing your poster in a DOI repository like Zenodo extends the lifespan of your poster beyond the conference, reaching audiences who…
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Reposted by Wenfei Xian (冼文飞)
Sophien Kamoun @kamounlab.bsky.social · 12/03/2024
Quizás, Quizás, Quizás #EffectorWisdom youtu.be/CmLNM6WHUHc?...
youtu.be
Gaby Moreno - "Quizás, Quizás, Quizás" | LIVE at The Kennedy Center
Gaby Moreno performs "Quizás, Quizás, Quizás" LIVE at the Kennedy Center.Watch the full concert: https://www.youtube.com/watch?v=qkBexC-n0DsSubscribe to The ...
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Reposted by Wenfei Xian (冼文飞)
Greg Priest @gregpriest.bsky.social · 09/03/2024
New study gives support to the “RNA World” hypothesis. An RNA has been synthesized that can replicate other RNA, showing an in-principle mechanism for how it could have worked. #evobio 🦫🦋 🗃️🧠 🌱🐋🧪🌎
pnas.org
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...
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Reposted by Wenfei Xian (冼文飞)
Sophien Kamoun @kamounlab.bsky.social · 08/03/2024
For funders, departments, and institutions: Consider preprints and their reviews in evaluations for funding, hiring, degree requirements, fellowship eligibility, tenure, and promotion. #preprintreview journals.plos.org/plosbiology/...
journals.plos.org
Recommendations for accelerating open preprint peer review to improve the culture of science
As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. This Consensus View issues a call to action to accelerate the growing momentum of p...
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Reposted by Wenfei Xian (冼文飞)
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 06/03/2024
Are you constructing genome graphs, and are you wondering how different graphs compare to each other? Then check out Sebastian Vorbrugg's Gretl - Variation GRaph Evaluation TooLkit! www.biorxiv.org/content/10.1...
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Reposted by Wenfei Xian (冼文飞)
Space Telescope Science Institute @stsci.edu · 04/03/2024
🔭 🧪 Two teams using the James Webb Space Telescope peered across space and time to learn secrets of strangely bright GN-z11 and its enormous black hole. GN-z11 is one of the youngest and most distant galaxies ever observed: webbtelescope.pub/3IiTZtG
A rectangular image with thousands of galaxies of various shapes and colors on the black background of space. Some are noticeably spirals, either face-on or edge-on, while others are blobby ellipticals. Many are too small to discern any structure. One prominent foreground star at top center features Webb’s signature 8-point diffraction spikes. At lower right, a small region is highlighted with a white box. Vertical lines extend upward like a cone to the bottom corners of a larger box at upper right, showing a zoomed in version of the highlighted area. The pullout features a galaxy labeled GN-z11, seen as a fuzzy yellow dot. Above it is another galaxy, seen as a fuzzy red oval.
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Wenfei Xian (冼文飞) @wenfeixian.bsky.social · 03/03/2024
Mr. 40,000 points! www.nba.com/news/lebron-...
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Reposted by Wenfei Xian (冼文飞)
Dani Rosado @drosado.bsky.social · 28/02/2024
How did we lose our tails? Blame it on the Alu! Really interesting work lead by @itaiyanai.bsky.social 🧪 #Science #EvoDevo
nature.com
On the genetic basis of tail-loss evolution in humans and apes - Nature
An insertion of an Alu element into an intron of the TBXT gene is identified as a genetic mechanism of tail-loss evolution in humans and apes, with implications for human health to...
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Wenfei Xian (冼文飞) @wenfeixian.bsky.social · 17/02/2024
I couldn't help but feel my eyes well up with tears
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Reposted by Wenfei Xian (冼文飞)
Adam Phillippy @aphillippy.bsky.social · 08/02/2024
Our current record is 40 out of 46 diploid chromosomes in T2T scaffolds straight from Verkko. We are closing in on the routine assembly of complete, personalized human genomes!
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Axel Künstner @knstnr.bsky.social · 07/02/2024
What is the main force in evolution? Selection or drift? academic.oup.com/gbe/article/...
academic.oup.com
Half a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution
Abstract. The neutral and nearly neutral theories, introduced more than 50 yr ago, have raised and still raise passionate discussion regarding the forces govern
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Reposted by Wenfei Xian (冼文飞)
Bluesky @bsky.app · 06/02/2024
You can now sign up for Bluesky without an invite! 🎉 bsky.social/about/blog/0...
bsky.social
Join Bluesky Today (Bye, Invites!) - Bluesky
Sign up for Bluesky! No invite code required.
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Reposted by Wenfei Xian (冼文飞)
Adrian @aconga.bsky.social · 04/02/2024
I am happy to announce that our story on transposable elements in Thlaspi arvense has been published in PLOS Genetics 🥳. Want to know how TEs are shaping the genomic landscape of this future oilseed crop? Have a look: journals.plos.org/plosgenetics... #TEworldwide 🧬🌿
journals.plos.org
Transposon dynamics in the emerging oilseed crop Thlaspi arvense
Author summary Transposable elements (TEs) are often considered genomic parasites, but they can also generate phenotypic novelty that helps organisms to adapt to new environments. To understand how TE...
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Wenfei Xian (冼文飞) @wenfeixian.bsky.social · 31/01/2024
When you have high-quality sequencing data, don't forget about the chloroplast genome🌵 Thanks Detlef! @plantevolution.bsky.social
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 24/01/2024
High-throughput selection of human de novo-emerged sORFs with high folding potential www.biorxiv.org/content/10.1101/202…
biorxiv.org
High-throughput selection of human de novo-emerged sORFs with high folding potential https://www.biorxiv.org/content/10.1101/2024.01.22.576604v1
De novo genes emerge from previously non-coding stretches of the genome. Their encoded de novo prote
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 25/01/2024
GTDrift: A resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes www.biorxiv.org/content/10.1101/202…
biorxiv.org
GTDrift: A resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes https://www.biorxiv.org/content/10.1101/2024.01.23.576799v1
We present GTDrift, a comprehensive data resource that enables explorations of genomic and transcrip
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 26/01/2024
Anti-gene oligonucleotides targeting Friedreichs ataxia expanded GAA:TTC repeats increase Frataxin expression www.biorxiv.org/content/10.1101/202…
biorxiv.org
Anti-gene oligonucleotides targeting Friedreichs ataxia expanded GAA:TTC repeats increase Frataxin expression https://www.biorxiv.org/content/10.1101/2024.01.25.577034v1
Friedreichs ataxia (FRDA) is a progressive, autosomal recessive ataxia caused, in the majority of ca
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Reposted by Wenfei Xian (冼文飞)
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 24/01/2024
REPrise: de novo interspersed repeat detection using inexact seeding www.biorxiv.org/content/10.1101/202…
biorxiv.org
REPrise: de novo interspersed repeat detection using inexact seeding https://www.biorxiv.org/content/10.1101/2024.01.21.576581v1
Motivation: Interspersed repeats occupy a large part of many eukaryotic genomes, and thus their accu
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