Hi everyone! I'm excited to announce that our lab at UW will soon be recruiting a postdoc to work on DNA methylation signatures in rare disease. This will be a mostly computational position. Please share and reach out if interested! millerlaboratory.com

Dr. @danrdanny.bsky.social and his team at @brotmanbaty.bsky.social have demonstrated a "sample-to-sequence" workflow for processing DNA isolated from cell culture, whole blood, and solid tissue. Learn more about this “hands-off” approach, with minimal manual intervention: https://bit.ly/4byIvBP

In honor of ASHG week (since I won’t be there), see "Choose your human genome reference wisely", in which Vivien Marx interviewed me @fergalmartin.bsky.social @lh3lh3.bsky.social @danrdanny.bsky.social @heidirehm.bsky.social and others on the state of the human reference rdcu.be/eJejg 🧵[1/10]

Thank you Dr. Danny Miller @danrdanny.bsky.social for hosting, and fantastic job Dr. Mastrorosa @fkma.bsky.social! @uwgenome.bsky.social brotmanbaty.org/news/long-re...

Literal case in point: we worked with @danrdanny.bsky.social (and transfusion medicine teams across two organizations) to use long-read WGS to solve the case of an untransfusable patient. #hemesky #medsky doi.org/10.1111/trf....

Long‐read DNA sequencing resolves a rare case of alloimmune hemolysis mimicking autoimmune hemolysis

Background Immune hemolytic anemia poses a significant challenge in transfusion medicine, as identification of underlying alloantibodies can be masked by warm and/or cold autoantibodies. This increa...

doi.org

Kerry Lannert@klannert.bsky.social · 11mo ago

Whole genome sequencing has gotten *shockingly* cheap, and analysis tools are sophisticated enough to generate a clinically-actionable result faster than traditional DNA sequencing methods. This is a huge leap for diagnosing rare genetic conditions.

One never knows the power and persuasion of elementary school teachers. Jonas ("Gus") Gustafson's fifth grade instructor 'allowed me to establish a life-long knack and passion for STEM.’ @uwmedicine.bsky.social @danrdanny.bsky.social brotmanbaty.org/news/promisi...

Interested in SV calling from LRS data but overwhelmed by the 25,000 variants you're sorting through? Check out needLR! Gus just updated it today to include SV calls from 450 1000 Genomes samples (900 haplotypes), vcf output, and much more. github.com/jgust1/needLR

GitHub - jgust1/needLR: A structural variant filtering and prioritization tool for long-read sequencing data

A structural variant filtering and prioritization tool for long-read sequencing data - jgust1/needLR

github.com

Has anyone had luck submitting a paper without submitting all author names on the paper? I am tired of spending an hour or more adding people to a journal submission site just to have the paper editorially rejected the next day... I know some journals have forms you can upload, but some do not.

I am very sad to share that Scott Hawley passed away this morning. Scott was my graduate advisor and no other person had such a positive impact on my life. I will miss him dearly.

HunterLab.bsky.social@hunterlab.bsky.social · 2y ago

Sadly, our colleague and friend Scott Hawley passed away this morning. He was an irreplaceable presence and force for good in the meiosis an Drosophila communities and will be sorely missed.

I never knew what it meant to go on a life changing trip until now. I just spent an amazing week in Nairobi teaching genetics to some truly wonderful physicians and seeing kids with suspected genetic conditions. It felt all the more special to have been there on Martin Luther King Jr. Day.

A homozygous SVA retrotransposon insertion is discovered to be likely the most common mutation in ASPA (encodes aspartoacylase) underlying Canavan disease. 1/ Gonzalez, Bell, et al. medRxiv www.medrxiv.org/content/10.1...

A Diagnostic Blind Spot: Deep intronic SVA_E Insertion identified as the most Common Pathogenic Variant Associated with Canavan Disease

Canavan disease (CD) is a neurodegenerative disorder caused by biallelic disease-causing variants in the ASPA gene. Here, we utilized long-read sequencing (LRS) to investigate eight individuals clinic...

medrxiv.org

Been looking forward to sharing this for a long time! Great collaboration with folks from across the world in which we identified a SVA_E insertion missed by standard clinical testing in individuals with Canavan disease, an early onset neurodegenerative disease. www.medrxiv.org/content/10.1...

A Diagnostic Blind Spot: Deep intronic SVA_E Insertion identified as the most Common Pathogenic Variant Associated with Canavan Disease

Canavan disease (CD) is a neurodegenerative disorder caused by biallelic disease-causing variants in the ASPA gene. Here, we utilized long-read sequencing (LRS) to investigate eight individuals clinic...

medrxiv.org

Fine, this job isn’t all that terrible…

Day 4 and 5 of computational genomics at CSH: students giving their project pitches and the view from my grant writing nest.

Your feel-good video for today. Dick Van Dyke at 99. www.youtube.com/watch?v=o4Ol...

Coldplay - ALL MY LOVE (Official Video) (Directors' Cut)

YouTube video by Coldplay

youtube.com

Day 2 of Computational Genomics at Cold Spring Harbor during the intro to UNIX session. 24 great students, 5 amazing TAs, fantastic lectures, and a few instructors who mostly complain about the coffee.

Biology of Genomes 2025 is coming up: - meeting dates: May 6 - 10, 2025 - abstract deadline: Feb 14, 2025 We hope to see you there for another great meeting with a fantastic speaker lineup! meetings.cshl.edu/meetings.asp...

Biology of Genomes

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

meetings.cshl.edu

A vertical takeoff of life science with #AI LLLMs. Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks! Unprecedented progress, reviewed in the new Ground Truths erictopol.substack.com/p/learning-t...

Amazing story

Jeremy Berg@jeremymberg.bsky.social · 2y ago

A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.

Good read about how the NIH functions. After 2 years as a new investigator I only now feel like I am starting to understand the process. This is one of the challenges for new investigators: why is the learning curve so steep?

Sasha Gusev@sashagusevposts.bsky.social · 2y ago

I wrote about the National Institutes of Health and the various serious and unserious proposals for NIH reform that have been floating around. It is important to understand how this agency actually functions and point criticism at the right problems. A short 🧵:

Show me a worse fortune for an early career researcher…

I love the starter packs, but adding people is a giant pain in the ass. Is there an easier way to add someone beyond editing it through your profile?

This time of year is getting close, folks! Just saying.

I created a long-read sequencing starter pack. I'm still finding people on here, so apologies if I missed you. Please suggest people who should be added and I'll add them! go.bsky.app/JGkefsJ

I made a starter pack of folks affiliated with UW Genome Sciences (past and present) go.bsky.app/L8RAbiJ It's fairly sparse for now, so please let me know if you'd like to be added!

UW Genome Sciences

Join the conversation

go.bsky.app

A classic chart by Max Roser: The rise and fall in smoking and lung cancer mortality over the 20th century.

Paper accepted…with no revisions! Been a minute since that happened. Lucky for excellent collaborators and a straightforward story.

One of my favorite facts about today's Nobel: "She was on track to become a full professor, but grant rejections led to her being demoted by the university in 1995. ... Her persistence was noted as exceptional against the norms of academic research work conditions." en.wikipedia.org/wiki/Katalin...

Our first cover! We got the cover of the October issue of G3 for our Acomys cahirinus genome! academic.oup.com/g3journal/is...

Do you create computational techniques to study genome biology or disease? In the 2nd year of our comp. genomics hiring initiative, @uudbmi is recruiting computational genomics faculty. Deadline=Nov. 10. Please share. utah.peopleadmin.com/postings/151...