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Jae Young Choi @jychoi.bsky.social · 16d

If you're interested in our method please check out the study and the method on github.
github.com/jaeyoungchoi...

GitHub - jaeyoungchoilab/Topsicle: Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read.

Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read. - jaeyoungchoilab/Topsicle

github.com

Jae Young Choi @jychoi.bsky.social · 16d

Details of our study can be found in my previous threads from our biorxiv preprint.
bsky.app/profile/jych...

Jae Young Choi @jychoi.bsky.social · Jul 15

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...

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data

Telomeres protect chromosome ends and its length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many b...

www.biorxiv.org

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Jae Young Choi @jychoi.bsky.social · 16d

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...

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data - Genome Biology

Telomeres protect chromosome ends and their length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many...

doi.org

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Jae Young Choi @jychoi.bsky.social · Jul 30

Toxin antidote system found in speciation research is good examples of this.

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Reposted by Jae Young Choi

Li Zhao @lizhao.bsky.social · Jul 15

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.

Gene regulatory networks and essential transcription factors for de novo-originated genes

Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...

rdcu.be

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Jae Young Choi @jychoi.bsky.social · Jul 15

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...

GitHub - jaeyoungchoilab/Topsicle: Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read.

Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read. - jaeyoungchoilab/Topsicle

github.com

Jae Young Choi @jychoi.bsky.social · Jul 15

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.

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Jae Young Choi @jychoi.bsky.social · Jul 15

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.

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Jae Young Choi @jychoi.bsky.social · Jul 15

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

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Jae Young Choi @jychoi.bsky.social · Jul 15

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.

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Jae Young Choi @jychoi.bsky.social · Jul 15

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

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Jae Young Choi @jychoi.bsky.social · Jul 15

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

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Jae Young Choi @jychoi.bsky.social · Jul 15

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

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Jae Young Choi @jychoi.bsky.social · Jul 15

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...

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data

Telomeres protect chromosome ends and its length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many b...

www.biorxiv.org

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Jae Young Choi @jychoi.bsky.social · Jun 28

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!

Jae Young Choi @jychoi.bsky.social · Jun 28

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.

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Jae Young Choi @jychoi.bsky.social · Jun 28

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.

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Jae Young Choi @jychoi.bsky.social · Jun 28

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*

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Jae Young Choi @jychoi.bsky.social · Jun 28

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.

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Jae Young Choi @jychoi.bsky.social · Jun 28

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...

GitHub - jaeyoungchoilab/Topsicle: Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read.

Topsicle utilizes abundance of telomere pattern k-mers to estimate telomere length in long read. - jaeyoungchoilab/Topsicle

github.com

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Jae Young Choi @jychoi.bsky.social · Jun 25

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Jae Young Choi @jychoi.bsky.social · Jun 19

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!

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Jae Young Choi @jychoi.bsky.social · Jun 17

@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.

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Jae Young Choi @jychoi.bsky.social · Jun 17

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

Monkeyflower (Mimulus) uncovers the evolutionary basis of the eukaryote telomere sequence variation

Author summary One of the most fascinating phenomena in evolutionary biology is the rapid evolution of molecular complexes with conserved functions across the tree of life. Studying these complexes ha...

journals.plos.org

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Reposted by Jae Young Choi

Jill Hamilton @jillahamilton.bsky.social · Dec 11

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

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