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.

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

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

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.

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!

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!