Wonder which tandem repeat genotyper to use on your Oxford Nanopore genomes? We benchmarked 7 tools on >100 ONT genomes. We assessed usability, assembly concordance, Mendelian consistency, and sensitivity to pathogenic expansions. www.biorxiv.org/content/10.6... 🖥️ 🧬 @cubiomedinfo.bsky.social

🧬 Ever wonder how fast your DNA changes from one generation to the next? @hdashnow.bsky.social and her team explored how quickly the human genome mutates by analyzing DNA from four generations of a single family. Dive into this video from @nature.com ⤵️

How quickly do humans mutate? Four generations help answer the question

YouTube video by nature video

youtu.be

A new article from Laurel Hiatt and @hdashnow.bsky.social describing STRchive is now available at Genome Medicine. genomemedicine.biomedcentral.com/articles/10.... Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci." strchive.org

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine

Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...

genomemedicine.biomedcentral.com

The strchive.org paper is out!! The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases. 🖥️ 🧬 link.springer.com/article/10.1...

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine

Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...

link.springer.com

I am excited to present STRchive.org v2! A resource for tandem repeats associated with Mendelian disease. We have resigned the website, added new loci, streamlined our data for easier reuse, added more detailed citations, presented population frequency data and more!

STRchive

An archive of STRs associated with human diseases

strchive.org

I’m launching a small but mighty starter pack for Academic Research Moms- those of us navigating the travails of parenthood and academic careers- and those who support them! Aka 💪 ARMy bsky.app/profile/did:...

Enjoying all the tandem repeat fun at #ASHG24? The Dashnow lab is hiring software developer/data analyst roles. Apply by Nov 13 for best consideration dashnowlab.org 🖥️ 🧬

Dashnow Lab

This is the website for the Dashnow Lab. We do computational genomics in the Department of Biomedical Informatics at the University of Colorado Anschutz Medical Campus.

dashnowlab.org

Very cool new work by @htanudisastro.bsky.social on the contribution of tandem repeat variants to gene expression in single cells! Check it out.

Hope Tanudisastro@htanudisastro.bsky.social · 2y ago

📢 New preprint alert: Excited to share our deep dive into the role of tandem repeats (TRs) in single-cell gene expression across the immune system, using WGS and scRNA-seq data from 1,790 individuals and over 5 million blood cells! 🧬 🧵👇 #repeats #SingleCell 1/9

I am currently recruiting a computational postdoc in my lab at CU dashnowlab.org The candidate would develop and use computational genomics methods to understand the genetic underpinnings of rare diseases and increase diagnoses. Pay starts at $70k for recent PhD grads

Our review article, with Ira Deveson, @hdashnow.bsky.social, @dgmacarthur.bsky.social, on sequencing & characterising short tandem repeats is out in @NatRevGen! We delve into short read & long read STR genotyping tools and applications in rare disease & population genetics 🧬go.nature.com/48pWZix

Our paper was published today in Nature Biotech! www.nature.com/articles/s41... Tandem Repeat Genotyping Tool (TRGT) is a new method for genotyping tandem repeats in PacBio HiFi long reads. We used some nice algorithmic strategies to improve genotyping accuracy. 🖥️ 🧬

Characterization and visualization of tandem repeats at genome scale - Nature Biotechnology

A set of tools maps tandem repeats across complete genomes.

nature.com

My "Friends don't let friends make bad graphs" repository has reached 1000+ stars on GitHub! I can't believe it! Thanks everyone for the interest and support. Gonna add this to my CV. 😂😂😂 github.com/cxli233/Frie...

I'm looking for talented postdocs and staff scientists/software developers to join my lab at medschool.cuanschutz.edu/dbmi If you're fascinated by #RareDisease genomics, #STRs and computational methods, please get in touch! I'm at #ASHG2023 this week, and happy to chat. #hiring

We're hiring a new faculty member in Clinical Informatics! Read more and apply at the link. cu.taleo.net/careersectio...

I had NO idea this is a thing - great tip!!

jess m. 🌤️@jametc.bsky.social · 3y ago

If bluesky seems a bit "dead" to you, check in your feed settings that you don't have the minimum likes turned up to see replies. If you have that on, you're going to be missing the most recent comments that haven't accrued likes yet

Could you please add me to What's Science for 🖥️ 🧬? @danirabaiotti.bsky.social

Just launched: STRchive (Short Tandem Repeat Archive) A database of STRs associated with disease in humans. harrietdashnow.com/STRchive/ This is inactive development. Looking for feedback and collaborators!