A big week for the lab! Two new papers on how cells repair DNA double-strand breaks: one on getting NHEJ started in chromatin, one on processing the ends before ligation. Years of work by a fantastic team.

Hi #TEsky, please remember that we have an amazing community in the TransposonsWorldWide slack channel (join.slack.com/t/transposon...), which I encourage you to join. Another great resource is tehub.org. Please share !

Join TransposonsWorldwide on Slack

Slack is a new way to communicate with your team. It’s faster, better organized, and more secure than email.

join.slack.com

Bit late posting this... MicroFinder is now published in GigaScience: academic.oup.com/gigascience/....

MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes

AbstractBackground. Obtaining chromosomally complete genome assemblies across the tree of life is an important goal of biodiversity genomics. However, some

academic.oup.com

Sad news today, as I heard that my PhD advisor Jim Hamrick passed away. Jim was a passionate naturalist and was instrumental in early efforts to document and understand genetic diversity in plant species -- using allonyms to quantify diversity for hundreds of different species.

John Wares@johnwares.bsky.social · 3mo ago

Sad to report that my colleague Dr. Jim Hamrick - a giant in the early study of plant population genetics, though in these 2017 photos he was contributing to the understanding of *barnacle* diversity - has passed.

BREAKING: The blackout in Spain and Portugal in April 2025 did NOT happen because of renewables. The final ENTSO-E report on last year's Iberian blackout is out — and it's essential reading for anyone working on the energy transition. www.entsoe.eu/news/2026/03...

🚀 New lab preprint on #SexChromosomeTurnover is out on @arxiv.bsky.social Huge congrats to lab thesis student for submitting his PhD @fwovlaanderen.bsky.social fellowship: big milestone and fingers crossed 🤞 and to all students for the submissions🤞🤞 More to come soon… 🐸🧬 arxiv.org/abs/2602.23624

Sex chromosome stability and turnover across vertebrates: a developmental gene regulatory network perspective

Sex chromosomes have evolved repeatedly across the Tree of Life, yet their evolutionary fates differ strikingly among lineages. In mammals and birds, highly degenerated Y/W chromosomes have remained s...

arxiv.org

#TEsky EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis doi.org/10.1186/s128...

EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis - BMC Genomics

BMC Genomics - Transposable elements (TEs) are major components of plant genomes, shaping genome architecture, gene regulation, and evolutionary innovation. While the Extensive de novo TE Annotator...

doi.org

New paper with @vsudbrack.bsky.social. Using pop gen modelling, we show that partial selfing makes selection on tandem repeats more efficient, reducing the associated load across different scenarios. Thanks to @snsf.ch @dee-unil.bsky.social @fbm-unil.bsky.social ! www.nature.com/articles/s41...

The evolution of tandem repeat sequences under partial selfing and different modes of selection - Heredity

Heredity - The evolution of tandem repeat sequences under partial selfing and different modes of selection

nature.com

Regulatory sciences are criminally underappreciated in philosophy of science, especially considering the impact they have on our everyday lives. I'm glad the talented HyeJeong Han is working on changing that! There's much to learn about the roles of institutions in shaping research processes

Alejandro Fábregas-Tejeda@alejandrofabregastejeda.com · 9mo ago

In her latest 📃, HyeJeong Han argues that in regulatory science (e.g., 💊 regulation), economic considerations shape decisions to halt experimentation. She shows how costs become integrated into evidential standards & impact institutionalized judgments👇 link.springer.com/article/10.1... #philsci #HPS

nph.onlinelibrary.wiley.com/doi/10.1111/...

An angiosperm‐wide perspective on reproductive strategies and floral traits

Flowering plants have many modes of sexual reproduction, notably varying from selfing to outcrossing, and from bisexual flowers to individuals with separate sexes (dioecy). These reproductive modes ...

nph.onlinelibrary.wiley.com

orthogene: a Bioconductor package to easily map genes within and across hundreds of species www.biorxiv.org/content/10.6... #Rstats bioconductor.org/packages/ort...

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics #TEworldwide #TEsky www.sciencedirect.com/science/arti...

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics

Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

sciencedirect.com

🚨Hiring a postdoc! Are you interested in #evolutionarygenomics, #sexchromosomes, #transposableelements & #Sexspecific #recombination in 🐸🧬? Join my lab @vubrussel.bsky.social 🔹 @fwovlaanderen.bsky.social funded up to 3y 🔹 Deadline 10/3/2026 🔹 Start ~1/6/2026 Apply 👉: jobs.vub.be/job/Elsene-P...

Are you a postdoc in plant biology? 🌾🧪 We invite you to join a community of 500+ postdoctoral researchers around the world. plantpostdocs.com/join-us/

plantpostdocs.bsky.social@plantpostdocs.bsky.social · 9mo ago

New Year Greetings from the PlantPostdocs team to our fam🍀 This new year, join the club or refer us to your colleagues 🌱 To know more about what we do, scan the QR code or log onto plantpostdocs.com

Who among us hasn’t produced five pages of crappy writing and then considered defacing the keyboard? Very relatable.

This skeet will self destruct@pardoguerra.bsky.social · 9mo ago

Writing something about ML and the Infinite Monkey Theorem and found this which made me laugh.

Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT. www.sciencedirect.com/science/arti... 🧵1/7 🧪

Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel

The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, design…

sciencedirect.com

Up this week: Proteaceae. Flowers are 4-merous, stamens fused to the uniseriate perianth, 1 carpel with a long style & pollen presentation. This Gondwanaland family is found throughout the S. Hemisphere but is most diverse in Australia. 📷: Leucospermum sp/cv. #Proteaceae #Botany 🌾🧪🌱

'This video is the culmination of several yrs attempting to: (1) Figure out best practices for modeling ptn-ptn interactions; (2) Understand the outputs of programs like AlphaFold & adjacent software including quantitative metrics;(3) Communicate my thoughts to unwitting victims through workshops'

AlphaFold protein interaction modeling tutorial and workshop - the Node

This video is the culmination of several years attempting to: (1) Figure out best practices for modeling protein-protein interactions; (2) Understand the This video is the culmination of several years...

thenode.biologists.com

One of my concerns with AI-assisted research in biology is that we're already looking only in the lamplight and AI incentivizes us to narrow the beam. Seems like it's happening... www.nature.com/articles/s41...

Artificial intelligence tools expand scientists’ impact but contract science’s focus - Nature

Artificial intelligence boosts individual scientists’ output, citations and career progression, but collectively narrows research diversity and reduces collaboration, concentrating work in data-rich a...

nature.com

#TEsky Host Factors Promoting the LTR Retrotransposon Life Cycle in Plant Cells: Current Knowledge and Future Directions doi.org/10.3390/ijms...

searching a #postdoc for #theoretical research at the interface between #physics, #biology and #popgen to study the #evolution of plant self-incompatibility. @hebrewuniversity.bsky.social www.friedlander-lab.net see application link in next post. Please share with relevant candidates.

Aleksey Zimin presents EVIANN (Evidence-based Annotation) While it does not drastically increase the accuracy over existing tools, its speed is ultrafast, can use ONT transcripts, creates UTRs and lncRNAs. #Bioinformatics #Genomics #Coding #PAG33 #PAG2026

Are you working on ancient plant DNA? 🌿 We are organising a symposium on Ancient plant genomics at #SMBE2026 in beautiful Copenhagen 🇩🇰 Join Nathan Wales, Shuya Zhang, Marcela Sandoval Velasco, me, and our fantastic speaker Logan Kistler from the Smithsonian Institution. Help us spread the word!

My co-conspirator and fellow PhD student Lila writes for The Conversation about how plants have separate sexes, sometimes. Ever wondered something about plant sexual systems? How to start learning about it? I'd say start with this.

Plant sex life is more complicated than you probably imagine

The amazing variety of plant reproductive systems.

theconversation.com

🧵 Just out in Cell after more than 10 years in the making! 🎓 www.cell.com/cell/fulltex... Plants and animals evolve radically different body plans. Do they also operate under fundamentally different molecular evolutionary constraints during organ formation? @cellpress.bsky.social

The pardon for Hernandez makes an obvious & absolute mockery of each & every attempt to rationalise, or even justify, Trump's treatment of Maduro. I'm not sure this single, simple point can be stressed enough. Once again, he proves his critics right & reduces his supporters to epic moral corruption.

Have we been overstating the role of transposable elements in adaptation to local or rapidly changing environmental conditions? Happy to share my (somewhat unpopular?) opinion paper on this matter: www.sciencedirect.com/science/arti... Thanks to those who already shared the link!

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics

Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

sciencedirect.com

Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2 www.youtube.com/watch?v=u63o...

David's AlphaFold WorkShop 2026

YouTube video by David Fay

youtube.com

Buenos días, Hoy hace un año, el Dr.Hussam se puso delante de los tanques de Israel para impedir que atacaran el hospital Kamal. Está en la cárcel, sin cargos, ni juicio, desde entonces. No olvidemos a Palestina.