Danny Miller, MD, PhD
@danrdanny.bsky.social
CODA. Dad. Interested in genetics, long-read sequencing, and ultramarathon running. Assistant Professor at University of Washington. The command line is my happy place. https://millerlaboratory.com
Reposted by Danny Miller, MD, PhD
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]
October 13, 2025 at 8:14 PM
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]
Reposted by Danny Miller, MD, PhD
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...
@uwgenome.bsky.social
brotmanbaty.org/news/long-re...
September 25, 2025 at 5:19 PM
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...
@uwgenome.bsky.social
brotmanbaty.org/news/long-re...
Reposted by Danny Miller, MD, PhD
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....
#hemesky #medsky
doi.org/10.1111/trf....
September 17, 2025 at 3:31 PM
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....
#hemesky #medsky
doi.org/10.1111/trf....
Reposted by Danny Miller, MD, PhD
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...
@uwmedicine.bsky.social
@danrdanny.bsky.social
brotmanbaty.org/news/promisi...
April 21, 2025 at 10:09 PM
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...
@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
April 11, 2025 at 2:14 AM
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
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.
February 21, 2025 at 5:15 PM
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.
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.
January 31, 2025 at 3:54 PM
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.
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.
January 25, 2025 at 11:41 AM
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.
Reposted by Danny Miller, MD, PhD
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...
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...
www.medrxiv.org
December 23, 2024 at 4:59 AM
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...
Gonzalez, Bell, et al. medRxiv
www.medrxiv.org/content/10.1...
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...
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...
www.medrxiv.org
December 23, 2024 at 2:49 AM
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...
www.medrxiv.org/content/10.1...
Fine, this job isn’t all that terrible…
December 11, 2024 at 12:26 AM
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.
December 8, 2024 at 6:28 PM
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
www.youtube.com
December 7, 2024 at 4:12 AM
Your feel-good video for today. Dick Van Dyke at 99. www.youtube.com/watch?v=o4Ol...
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.
December 5, 2024 at 9:13 PM
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.
Reposted by Danny Miller, MD, PhD
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...
- 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
December 3, 2024 at 7:21 PM
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...
- 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...
Reposted by Danny Miller, MD, PhD
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...
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...
November 24, 2024 at 6:12 PM
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...
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
A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.
homer simpson from the simpsons is holding a cup in front of a picture
ALT: homer simpson from the simpsons is holding a cup in front of a picture
media.tenor.com
November 24, 2024 at 11:00 PM
Amazing story
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?
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 🧵:
Distinguishing real from invented problems with the NIH
How does the NIH work and where does it work well?
open.substack.com
November 24, 2024 at 6:00 PM
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?
Show me a worse fortune for an early career researcher…
November 21, 2024 at 3:22 AM
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?
November 19, 2024 at 1:03 AM
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?
Reposted by Danny Miller, MD, PhD
This time of year is getting close, folks! Just saying.
November 18, 2024 at 1:11 AM
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
November 11, 2024 at 5:05 AM
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
Reposted by Danny Miller, MD, PhD
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!
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
November 8, 2024 at 10:24 PM
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!
go.bsky.app/L8RAbiJ
It's fairly sparse for now, so please let me know if you'd like to be added!
Reposted by Danny Miller, MD, PhD
A classic chart by Max Roser:
The rise and fall in smoking and lung cancer mortality over the 20th century.
The rise and fall in smoking and lung cancer mortality over the 20th century.
October 27, 2023 at 9:08 PM
A classic chart by Max Roser:
The rise and fall in smoking and lung cancer mortality over the 20th century.
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.
October 24, 2023 at 4:44 AM
Paper accepted…with no revisions! Been a minute since that happened. Lucky for excellent collaborators and a straightforward story.