Cheryl Keller

311 Followers
157 Following
59 Posts

Director, Genomics Research Incubator at PSU, DNA 🧬sequencing, genomics and gene regulation, hematopoiesis. #SeqItAll

Runner, cyclist, and triathlete
Team Zoot ambassador

ORICD0000-0001-6594-0245
Google Scholarhttps://scholar.google.com/citations?user=vKBGdXEAAAAJ&hl=en
How long are folks storing all their old sequencing 🧬reads and processed data? At what point do you just leave it to NCBI via GEO/SRA and delete from local/cloud storage? We have SO MUCH DATA going back to ~2010 and storage is expensive. 😬 #genomics #sequencing
How long are folks storing all their old sequencing 🧬reads and processed data? At what point do you just leave it to NCBI via GEO/SRA and delete from local/cloud storage? We have SO MUCH DATA going back to ~2010 and storage is expensive. 😬 #genomics #sequencing

Seasonal news: The mistletoe genome has been sequenced! 🎄

It's the largest genome of any species from Britain and Ireland, 30 times as big as the human genome but with only 10 chromosomes. 😀

https://www.darwintreeoflife.org/news_item/2022-the-year-we-built-the-biggest-genome-in-britain-and-ireland/

The year we built the biggest genome in Britain and Ireland – Darwin Tree of Life

Sharing this in case it's useful: I find that students often have a hard time conceptualizing quantitative parameters in genomics and popgen.

Here is a draft version of a cheat-sheet that I put together for my winter-quarter human genetics class. It's also part of a book that I am slowly writing on human popgen.

Corrections and other comments very welcome

When no mRNA is expressed from an enhancer in given a cell type, how to directly measure the reporter expression? Single-cell quantitative expression reporters (scQers) developed by Shendure lab can solve this problem. Key designs: 1) A dual RNA cassette decouples the detection and quantification (oBC for detection and mBC for quantification). 2) oBC are circularized Pol III transcribed barcodes which expressed >150-fold higher steady-state levels. #singlecell #devbio
https://www.biorxiv.org/content/10.1101/2022.12.10.519236v1
Anopheles albimanus is a Potential Alphavirus Vector in the Americas

Despite its ecological flexibility and geographical co-occurrence with human pathogens, little is known about the ability of Anopheles albimanus to transmit arboviruses. To address this gap, we challenged An. albimanus females with four alphaviruses and one flavivirus and monitored the progression of infections. We found this species is an efficient vector of the alphaviruses Mayaro virus, O’nyong-nyong virus, and Sindbis virus, although the latter two do not currently exist in its habitat range. An. albimanus was able to become infected with Chikungunya virus, but virus dissemination was rare (indicating the presence of a midgut escape barrier), and no mosquito transmitted. Mayaro virus rapidly established disseminated infections in An. albimanus females and was detected in the saliva of a substantial proportion of infected mosquitoes. Consistent with previous work in other anophelines, we find that An. albimanus is refractory to infection with flaviviruses, a phenotype that did not depend on midgut-specific barriers. Our work demonstrates that An. albimanus may be a vector of neglected emerging human pathogens and adds to recent evidence that anophelines are competent vectors for diverse arboviruses.

AJTMH
"Teaching Science with the Genome Browser" https://genome.ucsc.edu/training/education/ is a great resource for teaching/demonstrating a variety of genomic principles using vignettes based upon the UCSC Genome Browser. Really well put together!
Educating with the Genome Browser

Since I'm new to spore.social, I figured I'd do another #introduction post.

Hello! I'm Jacquelyn (she/her). I'm a scientist researching the past, present, and future of Earth's #climate and #biodiversity. I'm also a science communicator, a professor at UMaine, and a podcaster (Warm Regards, and Jax & Phoebe Make a Planet).

In addition to my work and advocacy, I'm a dungeon master who loves video and tabletop board games, natural history, books, and hiking.

#inro #introductions

#introduction It's Li here. I'm a plant biologist. I study genomics, single cell, specialized metabolism, and gene regulation. I also develop and maintain R & data visualization resources on GitHub.

https://github.com/cxli233

cxli233 - Overview

R for statistical inference and data visualization in plant molecular biology | [email protected] - cxli233

GitHub

So @.joinmastodon got unbanned from Twitter.

This is the first tweet that they sent after the unbanning:

"As a company from eastern Germany, we know that building a wall to try and keep people from leaving isn't a good idea."

What a response!