If you're interested in using pangenome graphs for comparative genomics, check out my webinar, part of EMBL-EBI's "Concepts, methods, and resources in pangenomics" series, available on-demand: www.ebi.ac.uk/training/eve...

Yesterday, Nina Marthe, our wonderful PhD student with Matthias Zytnicky, resubmit our tool GrAnnoT, for pangenome variation graph annotation! @ird-fr.bsky.social @inrae-france.bsky.social @peercommunityin.bsky.social #pangenomics 💻 www.biorxiv.org/content/10.1...

My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...

We @uga_genetics are hiring a TT assistant professor in Human Genetics to investigate how genetic makeup influences an individual’s risks for diseases or responses to drugs and therapies. All research approaches will be considered. Please RT. ugajobsearch.com/postings/456597

When transposons jump, genomes diverge - even in cultured cells. I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)

C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]

Come be our head of bioinformatics at @mrc-lms.bsky.social ! Our bioinformatics team are closely involved with lots of interesting science and we love working with them. Topics inc. development, cancer, metabolism, aging, TEs (my favourite of course 😜) #TEsky lms.mrc.ac.uk/work/vacanci...

Kicked off a series on #Drosophila TE discovery and naming. The first post covers elements that predate the term "mobile element", and more. artemilin.dev/posts/te_nam...

I share this picture of a printed out genome every once in while. It just occurred to me: it's got to be cheaper to acquire a finished copy of your genome (high accuracy, phased, SV-resolved) than to print it as a collection of bound books. (back-of-envelope checks out - anyone done the math?)

We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)

Pangene, an innovative computational tool, maps gene orientation, order & copy-number changes across genomes. Applied to the human pangenome, it reveals both known variation & complex haplotypes. Read more: academic.oup.com/bioinformati...

An interesting editorial by @judithmank.bsky.social, with thoughts on the use and misuse of AI in academic publishing at @evolletters.bsky.social (and elsewhere).

~ 5 and 1/2 years ago, my then postdoc advisor @plantevolution.bsky.social gave me complete freedom to assemble a team and interrogate NLR diversity in pangenomic context. We used @pacbio.bsky.social CCS and Iso-Seq, to annotate genomes with pathogen-challenged transcriptome. We then manually.....

Very impressive demonstration of the rise of China as a scientific superpower in crop research! All papers on #crop genetics and genomics in the latest issue of Nature Genetics were produced by scientists working at Chinese research institutes. TOC: www.nature.com/ng/volumes/5...

New Paper! In 2019, my first dissertation chapter revealed complicated polyploidies in the cotton family (Malvaceae) but we lacked the tools and genomes to truly understand it. Now with better genomes and improved methods, it's much more complicated than we thought. www.nature.com/articles/s41...

“In the heart of Illinois, while researching wildlife disease, I made a discovery that stunned me: More than half of the raccoons I sampled were infected with Trypanosoma cruzi, the parasite that causes Chagas’ disease… It’s here, in the United States, spreading silently in wildlife.”

Looking forward to this new installment of the Woods Hole Mobile DNA Meeting! Fantastic program, laid-back atmosphere, and gorgeous setting at the Marine Biological Laboratory ⛵️🪼🐋 Abstract submission closes Aug 7 but registration after that date is possible. www.eventsquid.com/event.cfm?ev...

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

My colleague David Garfinkel is looking for a postdoc to join our NIH-funded project on the “Evolution of Retrotransposon Control Mechanisms” More info here: reporter.nih.gov/search/u7dKr.... The official job listing can be found here: www.ugajobsearch.com/postings/437... Please repost! #TEsky

Pls. share widely Calling all transposon fans & lovers of genetic innovation MOBILE GENOME welcomes you in Heidelberg, Nov. 4–7 2025 → Vibrant & friendly community → Cutting-edge talks from mechanisms to physiology → Plenty of surprises (TEs never stop innovating) submit abstract by July 29

My colleague David Garfinkel is looking for a postdoc to join our NIH-funded project on the “Evolution of Retrotransposon Control Mechanisms” More info here: reporter.nih.gov/search/u7dKr.... The official job listing can be found here: www.ugajobsearch.com/postings/437... Please repost! #TEsky

🦟 Bioinformatics Research Scientist position open in my lab in Nice (FR) to study Aedes mosquito retrotransposons & their interactions with arboviruses collab w/ @salehlabparis.bsky.social & @lambrechtslab.bsky.social Apply: euraxess.ec.europa.eu/jobs/359830 Please boost! #ArboRetro #Bioinformatics

@brunolemaitre.bsky.social once told me not to trust big claims from papers with no follow-up work. People have likely tried and failed to replicate, but not published negative results. One of the best pieces of scientific advice I’ve ever received.

The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field? That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience A 🧵 1/n

So what are you to do when you find that some random website like @dailyimagesde, or @dailypicturesn, or @DailyFramesnet is infringing on your copyrights? 8/n

Update! I challenged @dailyimagesde’s spurious infringement claim with their domain registrar and won. I can’t prove @colossal, @BenLamm, or anyone else was responsible for this obvious harassment. But let's use this opportunity to learn how to seize back our copyrights. 1/n

For the next @jobim2025.bsky.social we will have posters and presentations from our various resources to work with #pangenome #graphs: annotation, manipulation, indexing, diversity and so on... Indeed we have plenty of them, and they are all gathered in one suite: the GraSuite !

The SMBE Lifetime Contribution Award winner is Chung-I Wu. ⭐ 2025 Winners: members.smbe.org/news/Details... 📄 Information on the Faculty Awards: www.smbe.org/faculty-awards

Seeing this make the rounds, thought I would bring back this blog post (remember those?) on these matters from back in the day from Casey Bergman @caseybergman.bsky.social‬ : caseybergman.wordpress.com/2012/08/26/t...

Transposable element enthusiasts at #Evol2025, please come by posters I12 on 6/22 and E17 on 6/23 to chat about horizontal transfer of Ty elements in yeast and oliverlevine.bsky.social's new method to predict TE insertions in pangenomes.

The first paper of my PhD is now available as a preprint! 🎉 Transposable elements (TEs) don't just jump within fungal genomes, they also move extensively between species. In this study, we screened over 1,300 fungal genomes and found a conservative estimate of 5,500+ horizontal transfer events.

Very grateful to be able continue a very fruitful collaboration with David Garfinkel’s Lab on how new transposon control mechanisms evolve in the genus Saccharomcyes.

Michael Ashburner FRS was an influential figure in the fields of Drosophila genomics and early sequencing database initiatives such as @ebi.embl.org. Read about their contributions across genetics and bioinformatics in the new biographical memoir: buff.ly/f01zNat @geneticscam.bsky.social‬

Could horizontal transfer be abundant not just in bacteria but also in eukaryotes? A recent work by Pianezza R, Haider A, Scarpa A, Signor S and Kofer R finds 3 HTs of transposons in a mere 30years. academic.oup.com/mbe/advance-... #evolution #drosophila

Pangenome-aware DeepVariant https://www.biorxiv.org/content/10.1101/2025.06.05.657102v1

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

A new simulation pipeline enhances benchmarking of transposon polymorphism detection tools genomics.peercommunityin.org/articles/rec...

One of the fun things about having a bit of notoriety and a semi-rare last name is that people send me photos and other memories of distant family members... like this photo of a postcard of my great-grandfather, BG Alfred Andrews Starbird (1875-1956), on a horse:

The program for Evolution 2025 is now live! Talk schedules for both the virtual and in-person meetings can be found here: www.xcdsystem.com/evolution/pr... @sse-evolution.bsky.social @systbiol.bsky.social @asn-amnat.bsky.social #Evol2025

Clever new BUSCO-like method to evaluate the quality of pangenome graphs www.biorxiv.org/content/10.1...

Wonderful summary of the life and work of an incomparable scientist, whose contributions laid the foundation for genome biology and bioinformatics. Thank you Steve and Rachel for writing this piece 🙏

Rachel Drysdale and I prepared a biographical memoir for Michael Ashburner, now published at: royalsocietypublishing.org/doi/10.1098/...

Along with every geneticist I am a total Mendel groupie and this new figure (www.nature.com/articles/s41...) that shows the chromosome location and underlying basis of his allelic pairs moves me to near-tears. Oh, to fly back in time and show this to him ...

The rest of Mendel's alleles characterized! So, out of 7 traits, 3 caused by TE insertions!!! (though apparently there are two different green alleles, one cause by a TE insertion, but another a promoter deletion allele) www.nature.com/articles/s41...

It’s out! The evolutionary origins of yeast point centromeres uncovered! “Ancient co-option of LTR retrotransposons as yeast centromeres” www.biorxiv.org/content/10.1...

Excited to do a postdoc in beautiful Neuchatel / Switzerland🇨🇭? We have several postdoc positions open at the moment! Check our website for the full ads here: pathogen-genomics.org/jobs Happy to answer any question and please spread the word to anyone who might be interested!

Register today for the EMBO course on #genome sequencing, assembly, curation, and downstream analyses meetings.embo.org/event/25-gen...