sigmafacto.bsky.social
Shujun Ou
@sigmafacto.bsky.social
96 followers 54 following 16 posts
Spartan, Assistant Professor @OhioState. Trying to understand how plants co-evolve with TEs. Author of LTR_retriever, LAI, EDTA, panEDTA, TESS...
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
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.
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jul 27
Summer Grill Heave Of Ou Lab (SGHOOL) and families!
sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 9
The position is filled. Thank you all for helping to spread the word!
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
TESS is an open-source package developed by Dr. Chris Benson (Ohio State), Dr. Ting-Hsuan Chen (NZ Plant & Food) & Mr. Tianyu Lu (Ohio State Senior UG). The study is conceived with Drs. Susan Thomson and Cecilia Deng (NZ Plant & Food). Please try it out! /n github.com/cwb14/TESS/t...
GitHub - cwb14/TESS: A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction
A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction - cwb14/TESS
github.com
sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
Using TESS and parameter sweep, we were able to approximate the TE dynamics of these three rust fungus genomes, revealing the two-stage evolution of myrtle rust (A. psidii), with a long-lasting genome expansion transitioned to aggressive contraction ~1.2 million generations ago.
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Shujun Ou @sigmafacto.bsky.social · Jun 7
We selected three extreme cases, being fast insertion/fast deletion/stable genome (Cronartium ribicola), slow insertion/slow deletion/stable genome (Puccinia coronata), and fast insertion/slow deletion/obese genome (Austropuccinia psidii), typical of eukaryotic genome dynamics.
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Shujun Ou @sigmafacto.bsky.social · Jun 7
What can TESS achieve? We used it to study the genome evolution dynamics of Pucciniomycotina, a subdivision of rust fungi with 58 high-quality genomes available and sizes varying from 20 Mb to 1018 Mb, mostly due to TE dynamics!
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
The PrinTE component of TESS makes genomes live on silicon chips! It can simulate TE insertions and deletions at any rates and dynamics, including complete deletions or creation of solo LTRs, and allow genomes to evolve forward in time. Here is one simulation of a digital genome:
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
The third mode of TEgenomeSimulator can simulate genomes with almost identical size, TE content, TE length distribution, and a normalized TE divergence (for ease of modeling) to real genomes - essentially digital replicas. This powerful mode allows in-silico genome evolution!
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
The TEgenomeSimulator component has three modes, which can simulate genomes representing snapshots of TE evolution at different stages: ancient expansion, recent expansion, long-lasting burst, and short burst.
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
The RandSeqInsert component can simulate TIR transposon insertions using a live-updated, high-performance AVL tree structure. It takes user-provided TIR libraries and allows setting varying lengths of target site duplications and nested insertions that mimic true TE insertions.
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
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.
1 13 24
sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Jun 7
At this point, we still need human experts to distinguish AI-generated papers from authentic manuscripts, and even this fails quite frequently. Without peer review as gatekeepers, manuscript posting may become somewhat like blogging. Non-specialists will have a hard time distinguishing make-ups.
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Apr 24
I start to screen for interview candidates. If you are interested, please hurry up!
sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Apr 10
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
sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Apr 10
The job is at Ohio State University located in Columbus, Ohio, a very commutable, affordable, and livable city with enriched food, nature, and culture. We are a fun, diverse group that care for each other and promote individual success. Please help to repost! Thank you for your attention! 3/3
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Shujun Ou @sigmafacto.bsky.social · Apr 10
The position will need to drive the project to the finish line, including pretty-plotting, additional analyses, and writing. If you are looking for a short, impactful project that will drive your career to the next level, please give us a shot :) 2/n t.co/BENTN756GZ
https://osu.wd1.myworkdayjobs.com/en-US/OSUCareers/job/Post-Doctoral-Scholar_R103545-1
t.co
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sigmafacto.bsky.social
Shujun Ou @sigmafacto.bsky.social · Apr 10
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
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