We reengineered the TIR-Learner for 60-100 times faster de novo search of Terminal Inverted Repeat transposons. We completed annotating 579 vertebrate genomes in 4 hours! Kenji Gerhardt did all the heavy lifting for this "side project".

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2w ago

TIR-Learner v4: Accelerated annotation of terminal inverted repeat transposons https://www.biorxiv.org/content/10.64898/2026.07.21.739826v1

Well done @sigmafacto.bsky.social !!! Proud to have had a very small part in EDTA v2 for improved large-scale repeat annotations www.biorxiv.org/content/10.6...

EDTA v2: enabling scalable TE annotation in animal genomes

The Extensive de-novo TE Annotator (EDTA) automates transposable element annotation in plant genomes but lacks direct LINE/SINE detection, limiting its applicability to animal genomes. We present EDTA...

biorxiv.org

Interesting new preprint from the Ou lab, using long-read sequencing to characterize transcriptional initiation in LTR transposons in maize

bioRxiv Plant Bio@biorxiv-plants.bsky.social · 3mo ago

The gene-like promoter and transcription of LTR retrotransposons. https://www.biorxiv.org/content/10.64898/2026.05.08.723830v1

Summer Grill Heave Of Ou Lab (SGHOOL) and families!

I want to share our latest work on a forward simulation framework on transposable element evolution. The TE Evolution Simulation Suite, or TESS, contains three components that can simulate many scenarios of genome evolution under the impact of TEs.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

TESS: A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction https://www.biorxiv.org/content/10.1101/2025.06.04.657780v1

I start to screen for interview candidates. If you are interested, please hurry up!

Shujun Ou@sigmafacto.bsky.social · last yr.

Hello bluesky world! Newbee here! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n

Hello bluesky world! Newbee here! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n