Huh I remember seeing a similar thread at twitter eons ago. Is nature healing?
17.11.2025 19:10
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Huh I remember seeing a similar thread at twitter eons ago. Is nature healing?
I am looking to hire a postdoc interested in combining genetics and evolution to understand why telomeres vary so much in plants. My group has been developing Mimulus a genetic model for studying plant telomeres and we have really cool research brewing. Please check ad for detail. Deadline is 12/31.
A nice write-up on the latest paper from my lab: news.ku.edu/news/article...
More commentary to come!
#PlantBiology #Drought #Corn #Maize #Microbiome #PlantScience #SoilHealth #PlantHealth
If you're interested in our method please check out the study and the method on github.
github.com/jaeyoungchoi...
Details of our study can be found in my previous threads from our biorxiv preprint.
bsky.app/profile/jych...
Excited to share a new method developed from my group thats published at Genome Biology. This was an amazing effort by my grad student Linh @linhngk.bsky.social. We developed Topsicle, a method that analyzes long read data for telomere analysis and length measuring.
doi.org/10.1186/s130...
Toxin antidote system found in speciation research is good examples of this.
Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.
Topsicle can work on either Nanopore or Pacbio data. And you don't need to have a reference genome. Just get your FASTQ and analyze with Topsicle! Our package can be found on github. If you're interested in the telomere length of your organism please try!
github.com/jaeyoungchoi...
We also used our method on 8 human cancer cell lines and compared it to Telogator which is a method developed mostly for mammalian telomeres. And results shows that our method is well correlated with Telogator.
When we compare Topsicle estimates with gold standard direct estimates from Southern blots its fairly well correlated suggesting our method works pretty well. We tried our method in A. thaliana, maize, and monkeyflower and they all worked well.
Topsicle performs fairly well under simulated reads of varying sizes and error rates. Interestingly under simulated coverages we saw that the genome coverage didnt have too much of an effect on telomere length estimates
This is done by implementing a change point method. These are commonly used in electrical engineering to model signal intensity data and it also works well for our purpose. We implemented our approach into a program called Topsicle.
Because long reads can be noisy looking exact matching telomere repeat sequence (e.g. AAACCCT) can miss repeat matches. Instead we search for k-mers of different sizes to fill in the gaps. From here telomere length is measured by finding the point where theres a sudden drop in telo density
Instead we thought what about a genomics approach? Technically if a long read was sequenced from the telomere we should be able to use that read to estimate the telomere length. And thats what we did! We came up with a way to search for telomeric long reads
My lab is interested in understanding what drives the genetic variation in telomeres of plants. We are interested in telomere length variation and to study this we need to measure length of the telomere but this protocol is often difficult to implement in a typical lab. Think of Southern blots
I'm very excited to share a new method my grad student @linhngk.bsky.social and I have developed. Here's Topsicle a new computational method for analyzing long read sequencing data and estimate telomere length. Please see our preprint or this thread for detail!
www.biorxiv.org/content/10.1...
Please give it a try if you're interested in measuring the telomere length of the organism you long read sequenced. Hopefully the peer reviewed manuscript of our method will come out shortly!
And it performs fairly well against various error rates and genome coverage. We tested it against gold standard telomere length measurements made from several A. thaliana ecotypes and found it was highly correlated with Topsicle predictions as well.
Topsicle searches for long reads from the telomere and then uses those as candidate telomere reads. Then we quantify telomere repeats with k-mer analysis and identify the telomere-subtelomere boundary using change point analysis.
Traditional way of measuring telomere length is thru Southern blot but its a lost art not many know how to do. Instead we thought what about long read sequencing since long read from telomere could be used to identify the telomere and measure its length. So we developed Topsicle. *image not related*
Telomere length is a really interesting phenotype where despite having crucial roles in maintaining genome stability its length can vary alot between individuals and even between species. Why is that? Is a major question many like to answer.
I'd like to share a new method my grad student Linh and I have been developing called Topsicle. Do you have long read sequencing data and wondered what the telomere length of your organism is? If you're wondering then Topsicle is the tool for you!
github.com/jaeyoungchoi...
My group is at #Evol2025 to present everything about telomere evolution!
Surbhi Sat 11:15 will present Mimulus telomere molecular evolution
Linh Sat 12:00 will present Mimulus pangenome and telomeres
Joyce Sat poster board A7 is here as Undergraduate Diversity at Evolution
Please join us!
@surbhi02.bsky.social essentially pushed new techniques and technologies in our group and I feel like we are now an actual telomere biology lab! This work would not have been possible without the generous collaborators.
I'm very excited to share the first research paper from my lab! My postdoc Surbhi led this amazing study. We combined genomics, evolution, and biochemistry to explain how telomeres evolved in monkeyflowers. If you're into unusual chromosome evolution please read! @plos.org
tinyurl.com/bdeku44x
I am excited to announce that registration and abstract submission is now open for Forest Genetics 2025 – ‘Harnessing Genetic Diversity for Resilient Forests’. Join us in State College, Pennsylvania from June 23-27, 2025 - all are welcome! forestgeneticsconference2025.com #forestgenetics2025
Are you interested in a postdoc with both research and teaching? Please consider the NIH IRACDA fellowship at KU iracda.ku.edu. If interested I can sponsor especially if you're a plant biologist or evo biologist. Eligibility is limited to US citizen or PR. Please share!
My lab is looking for a postdoctoral scholar. See image or t.co/bdIxT8eE6n
If you're a plant geneticist or mol biologist and appreciate the wonders of evolution this is a position for you.
We can teach dry lab or genomics so plz consider if you want to learn a new skill!