Casey Bergman

Crushed to hear of Mark Batzer’s passing. He was the Boyd Professor at Louisiana State University. His influential research revealed how mobile elements shape the genomes of humans & other mammals. Mark’s personality, generosity & positivity were larger than life. He lifted everyone up. HUGE loss 💔

🍄Transposon traffic in the mycocosmos🍄
Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu....
#TEworldwide

onlinelibrary.wiley.com/doi/full/10....

@cedricfeschotte.bsky.social

The Tangled Field: Barbara McClintock's Search for the Patterns of Genetic Control Buy The Tangled Field: Barbara McClintock's Search for the Patterns of Genetic Control on Amazon.com ✓ FREE SHIPPING on qualified orders

Hey, good folks of #TEsky—
Looking for good recent review, suitable for undergrads, of the fnxns of transposable elements in the genome, for class session on the nonlinear, highly regulated, 4D nucleome. Suggestions welcome!

(I'm the author of the "other book" on Barbara McClintock)

TIA!

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...

We are excited to invite abstract submissions for talks and posters for the 2026 Ecology and Evolution of Infectious Diseases meeting at Virginia Tech (June 2-4). Abstract submissions should be made by February 3, 2026 for consideration, using the google form here: cpe.vt.edu/eeid2026/abs...

Hivemind: has anyone had a response from #NCBI about submissions started prior to the government shutdown?

Hivemind: has anyone had a response from #NCBI about submissions started prior to the government shutdown?

I have created a bot account. This bot will receive information about newly uploaded #Drosophila papers from pubmed and will automatically post every hour. If you find any bugs, please let me know!

@fly-broadcast.bsky.social

This helps me understand why PERL was adopted so quickly in bioinformatics. Compared to AWK, it must have seemed like the future.

Congratulations to Richard Durbin on being awarded our Genetics Society Medal!

Locityper enables targeted genotyping of complex polymorphic genes - Nature Genetics Locityper is a general-purpose genotyper that can efficiently genotype and analyze a diverse set of genes, such as hyperpolymorphic HLA genes, using both short-read and long-read whole-genome sequenci...

💡 Novel work supported by HPRC members highlights Locityper, a tool bringing accurate genotyping to some of the most challenging regions of the human genome.

Fast and precise, it outperforms current pipelines and scales to biobank-sized cohorts.

More at:
www.nature.com/articles/s41...

Dynamics of genome evolution in the era of pangenome analysis Long-read sequencing and telomere-to-telomere (T2T) assemblies have enabled the generation of pangenomes that capture genetic diversity beyond single reference genomes. This review highlights how T2T ...

Thrilled to share our latest review! T2T assemblies are reshaping how we study genomic diversity. Pangenomes unlock structural variants, gene presence-absence, and genotype-phenotype relationship, across humans, plants, animals, and fungi.
www.cell.com/cell-genomic...

Beyond Wolbachia—Can a small molecule control insect reproduction? Kaur et al. demonstrate reduced histone acetylation as a key mechanism underpinning Wolbachia’s paternal-effect embryonic lethality trait in Drosophila melanogaster. Recapitulation of this trait by in...

#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years.

www.cell.com/cell-reports...

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...

Thanks very much!

Interesting, could you post a link to these slides. TIA!

GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph The increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. Pangenomes, encompassing the genomic inf...

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...

Remembering Hamilton O. Smith Hamilton O. Smith August 31, 1931 – October 25, 2025 It is with profound sorrow that we announce the loss of Hamilton O. Smith, M.D., a...

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

👏👏👏 Fantastic work, can’t wait to read!

Graphical abstract: The Drosophila OSC Genome as a resource for transposon and piRNA biology. The figure illustrates the workflow and key findings. Left: De novo genome assembly using Oxford Nanopore Technologies (ONT) long reads and Hi-C data generates a phased assembly distinguishing unique (blue) and repetitive (orange) sequences. Dot plot comparison between OSC-r1.01 and dm6 reference genomes shows overall synteny with extensive structural variation. Middle: A freely accessible UCSC genome browser session displays multi-omics data tracks including gene models, transposon insertions, chromatin accessibility, transcription, small RNAs, and histone modifications. Right: New insights into flamenco piRNA cluster biology reveal >730 kb transcribed from a single promoter without major splicing. Tethering assays demonstrate long-range silencing effects across the locus, and genome browser tracks show coordinated regulation of piRNA production, transcription, and chromatin state. This resource enables comprehensive studies of transposon regulation and piRNA pathway function in a widely-used Drosophila cell line.

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 🧵]

Head of Bioinformatics - MRC Laboratory of Medical Sciences We are recruiting for a Head of Bioinformatics to lead our Bioinformatics facility

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...

A photo of the first printout of the human reference genome presented as a series of books, displayed at the Wellcome Collection, London. Image taken from https://en.wikipedia.org/wiki/Reference_genome

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)