Aaron Quinlan (he/him)
@aaronquinlan.bsky.social
Origins and consequences of genome mutation; software for genomic discovery.
Prof. and Chair of Human Genetics at U. of Utah.
https://www.genetics.utah.edu/
http://quinlanlab.org
Prof. and Chair of Human Genetics at U. of Utah.
https://www.genetics.utah.edu/
http://quinlanlab.org
New lab photo for the first time in too many years. I am so proud of this team's curiosity, camaraderie, and collabative energy.
February 10, 2026 at 4:27 PM
New lab photo for the first time in too many years. I am so proud of this team's curiosity, camaraderie, and collabative energy.
Reminder that the abstract deadline for the Biology of Genomes meeting at CSHL is on Feb 13! We have a fantastic lineup of keynote speakers (Janet Kelso and Jonathan Pritchard) and session chairs. Submit your best science to this exciting and engaged meeting!
meetings.cshl.edu/meetings.asp...
meetings.cshl.edu/meetings.asp...
The 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
February 5, 2026 at 2:24 PM
Reminder that the abstract deadline for the Biology of Genomes meeting at CSHL is on Feb 13! We have a fantastic lineup of keynote speakers (Janet Kelso and Jonathan Pritchard) and session chairs. Submit your best science to this exciting and engaged meeting!
meetings.cshl.edu/meetings.asp...
meetings.cshl.edu/meetings.asp...
Reposted by Aaron Quinlan (he/him)
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
Common variation in meiosis genes shapes human recombination and aneuploidy - Nature
Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...
www.nature.com
January 21, 2026 at 9:14 PM
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
A new preprint from Peter Mchale and Michael Goldberg in my group on the latent biases inherent to current models of non-coding constraint.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
The performance of genetic-constraint metrics varies significantly across the human noncoding genome
A longstanding goal in human genetics is to prioritize noncoding loci that, when disrupted, lead to developmental disorders and other Mendelian traits. In pursuit of this goal, multiple metrics have been developed to distinguish neutrally evolving sequences from those subjected to purifying selection. These metrics are commonly evaluated genome-wide, e.g., by computing a precision-recall curve on windows tiling the entire noncoding genome. Here, we identify parts of the noncoding genome where these metrics significantly underperform relative to their genome-wide performance due to "bias" in the underlying models of neutral genetic variation and/or a low "signal-to-noise ratio" in the genetic data. The most extreme effects are found for Gnocchi (Chen et al. 2024), the performance of which declines as GC content increases. We suggest annotating constraint scores of noncoding genomic intervals with robust measures of the bias of the corresponding model, allowing users to gauge confidence in those scores. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, R01HG012252
www.biorxiv.org
January 29, 2026 at 3:28 PM
A new preprint from Peter Mchale and Michael Goldberg in my group on the latent biases inherent to current models of non-coding constraint.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Aaron Quinlan (he/him)
This is an important and information rich article. I wondered about the effects by Institute. The table below (which is snipped here but is in the article) has that info. Broken down by # of grants and $ amounts.
December 2, 2025 at 4:25 PM
This is an important and information rich article. I wondered about the effects by Institute. The table below (which is snipped here but is in the article) has that info. Broken down by # of grants and $ amounts.
All developed by @brent-p.bsky.social
December 2, 2025 at 1:17 PM
All developed by @brent-p.bsky.social
Get bedder v0.1.8 and r𝗲𝗮𝗱 𝘁𝗵𝗲 𝗱𝗼𝗰𝘂𝗺𝗲𝗻𝘁𝗮𝘁𝗶𝗼𝗻 here: github.com/quinlan-lab/...
We are looking for researchers to kick the tires, integrate bedder into their pipelines, and provide feedback on the Python functions, performance, and overall user experience! Please share and give us your feedback.
We are looking for researchers to kick the tires, integrate bedder into their pipelines, and provide feedback on the Python functions, performance, and overall user experience! Please share and give us your feedback.
Release Release v0.1.8 · quinlan-lab/bedder-rs
Changes in v0.1.8
Downloads
bedder-static-linux-x86_64: Static binary for Linux x86_64 (no dependencies required)
bedder-static-macos-x86_64-python3.13: macOS x86_64 binary built with Python 3.13
...
github.com
December 2, 2025 at 2:28 AM
Get bedder v0.1.8 and r𝗲𝗮𝗱 𝘁𝗵𝗲 𝗱𝗼𝗰𝘂𝗺𝗲𝗻𝘁𝗮𝘁𝗶𝗼𝗻 here: github.com/quinlan-lab/...
We are looking for researchers to kick the tires, integrate bedder into their pipelines, and provide feedback on the Python functions, performance, and overall user experience! Please share and give us your feedback.
We are looking for researchers to kick the tires, integrate bedder into their pipelines, and provide feedback on the Python functions, performance, and overall user experience! Please share and give us your feedback.
4. 𝗦𝗶𝗺𝗽𝗹𝗶𝗳𝗶𝗲𝗱 𝘀𝘆𝗻𝘁𝗮𝘅: We've streamlined the intersection logic, replacing complex flags like -wao, -f, and -r with clearer, modular options for defining intersection requirements.
Release Release v0.1.8 · quinlan-lab/bedder-rs
Changes in v0.1.8
Downloads
bedder-static-linux-x86_64: Static binary for Linux x86_64 (no dependencies required)
bedder-static-macos-x86_64-python3.13: macOS x86_64 binary built with Python 3.13
...
github.com
December 2, 2025 at 2:28 AM
4. 𝗦𝗶𝗺𝗽𝗹𝗶𝗳𝗶𝗲𝗱 𝘀𝘆𝗻𝘁𝗮𝘅: We've streamlined the intersection logic, replacing complex flags like -wao, -f, and -r with clearer, modular options for defining intersection requirements.
3. 𝗨𝘀𝗲 𝗼𝗳 𝗶𝗻𝗱𝗶𝗰𝗲𝘀 𝗳𝗼𝗿 𝗵𝗶𝗴𝗵 𝗽𝗲𝗿𝗳𝗼𝗿𝗺𝗮𝗻𝗰𝗲 𝗼𝗻 𝗹𝗮𝗿𝗴𝗲 𝗱𝗮𝘁𝗮 𝘀𝗲𝘁𝘀: bedder is engineered to utilize file indexing (e.g., VCF indexes), resulting in dramatically faster queries, especially when intersecting against massive indexed datasets like gnomAD.
Release Release v0.1.8 · quinlan-lab/bedder-rs
Changes in v0.1.8
Downloads
bedder-static-linux-x86_64: Static binary for Linux x86_64 (no dependencies required)
bedder-static-macos-x86_64-python3.13: macOS x86_64 binary built with Python 3.13
...
github.com
December 2, 2025 at 2:28 AM
3. 𝗨𝘀𝗲 𝗼𝗳 𝗶𝗻𝗱𝗶𝗰𝗲𝘀 𝗳𝗼𝗿 𝗵𝗶𝗴𝗵 𝗽𝗲𝗿𝗳𝗼𝗿𝗺𝗮𝗻𝗰𝗲 𝗼𝗻 𝗹𝗮𝗿𝗴𝗲 𝗱𝗮𝘁𝗮 𝘀𝗲𝘁𝘀: bedder is engineered to utilize file indexing (e.g., VCF indexes), resulting in dramatically faster queries, especially when intersecting against massive indexed datasets like gnomAD.
2. 𝗩𝗖𝗙 𝗜𝗻𝘁𝗲𝗴𝗿𝗮𝘁𝗶𝗼𝗻: For the first time, you can easily update VCF INFO fields based on interval overlaps, opening up new possibilities for variant annotation and processing.
Release Release v0.1.8 · quinlan-lab/bedder-rs
Changes in v0.1.8
Downloads
bedder-static-linux-x86_64: Static binary for Linux x86_64 (no dependencies required)
bedder-static-macos-x86_64-python3.13: macOS x86_64 binary built with Python 3.13
...
github.com
December 2, 2025 at 2:28 AM
2. 𝗩𝗖𝗙 𝗜𝗻𝘁𝗲𝗴𝗿𝗮𝘁𝗶𝗼𝗻: For the first time, you can easily update VCF INFO fields based on interval overlaps, opening up new possibilities for variant annotation and processing.
Here is a high-level summary of what is innovative about #𝗯𝗲𝗱𝗱𝗲𝗿:
𝗖𝘂𝘀𝘁𝗼𝗺 𝗟𝗼𝗴𝗶𝗰 𝘄𝗶𝘁𝗵 𝗣𝘆𝘁𝗵𝗼𝗻: bedder has a flexible Python interface that allows you to define custom functions to process intersection fragments on the fly. This enables custom analyses without the need for endless command-line options.
𝗖𝘂𝘀𝘁𝗼𝗺 𝗟𝗼𝗴𝗶𝗰 𝘄𝗶𝘁𝗵 𝗣𝘆𝘁𝗵𝗼𝗻: bedder has a flexible Python interface that allows you to define custom functions to process intersection fragments on the fly. This enables custom analyses without the need for endless command-line options.
Release Release v0.1.8 · quinlan-lab/bedder-rs
Changes in v0.1.8
Downloads
bedder-static-linux-x86_64: Static binary for Linux x86_64 (no dependencies required)
bedder-static-macos-x86_64-python3.13: macOS x86_64 binary built with Python 3.13
...
github.com
December 2, 2025 at 2:28 AM
Here is a high-level summary of what is innovative about #𝗯𝗲𝗱𝗱𝗲𝗿:
𝗖𝘂𝘀𝘁𝗼𝗺 𝗟𝗼𝗴𝗶𝗰 𝘄𝗶𝘁𝗵 𝗣𝘆𝘁𝗵𝗼𝗻: bedder has a flexible Python interface that allows you to define custom functions to process intersection fragments on the fly. This enables custom analyses without the need for endless command-line options.
𝗖𝘂𝘀𝘁𝗼𝗺 𝗟𝗼𝗴𝗶𝗰 𝘄𝗶𝘁𝗵 𝗣𝘆𝘁𝗵𝗼𝗻: bedder has a flexible Python interface that allows you to define custom functions to process intersection fragments on the fly. This enables custom analyses without the need for endless command-line options.
Developed in Rust for speed and efficiency, bedder is designed to overcome the analytical limitations of traditional interval-based tools by putting analytical flexibility directly into your hands.
Please read our detailed 𝗯𝗹𝗼𝗴 𝗽𝗼𝘀𝘁: quinlanlab.org/blogposts/be...
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Please read our detailed 𝗯𝗹𝗼𝗴 𝗽𝗼𝘀𝘁: quinlanlab.org/blogposts/be...
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Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
Developed in Rust for speed and efficiency, bedder is designed to overcome the analytical limitations of traditional interval-based tools by putting analytical flexibility directly into your hands.
Please read our detailed 𝗯𝗹𝗼𝗴 𝗽𝗼𝘀𝘁: quinlanlab.org/blogposts/be...
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Please read our detailed 𝗯𝗹𝗼𝗴 𝗽𝗼𝘀𝘁: quinlanlab.org/blogposts/be...
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We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
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Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
I was excited to be Dept. Chair as a way to serve, grow, and improve the department I love. The first year has certainly provided ample opportunities to learn the ropes of the role!
August 7, 2025 at 6:48 PM
I was excited to be Dept. Chair as a way to serve, grow, and improve the department I love. The first year has certainly provided ample opportunities to learn the ropes of the role!
Reposted by Aaron Quinlan (he/him)
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
June 10, 2025 at 4:27 PM
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Perspective on the impact of cuts to research funding from Jerry Kaplan and Dana Carroll, two science giants from the University of Utah. It highlights the storied history of the fantastic Dept. of Human Genetics that I now have the privilege of leading. www.sltrib.com/opinion/comm...
Voices: Federal funding cuts to genetic research will be devastating for years to come
Proposed cuts to the National Institutes of Health and the National Science Foundation “would cause immense and largely irreversible damage to the successful American scientific enterprise,” write Jer...
www.sltrib.com
July 8, 2025 at 5:40 PM
Perspective on the impact of cuts to research funding from Jerry Kaplan and Dana Carroll, two science giants from the University of Utah. It highlights the storied history of the fantastic Dept. of Human Genetics that I now have the privilege of leading. www.sltrib.com/opinion/comm...
Reposted by Aaron Quinlan (he/him)
Forbes: 'Hundreds Of NIH Staff Send Strong Letter Of Dissent To Their Bosses'
'In addition to Bhattacharya, the letter was sent to U.S. Health and Human Services Secretary Robert F. Kennedy Jr. and members of Congress who oversee NIH'
www.forbes.com/sites/michae...
'In addition to Bhattacharya, the letter was sent to U.S. Health and Human Services Secretary Robert F. Kennedy Jr. and members of Congress who oversee NIH'
www.forbes.com/sites/michae...
Hundreds Of NIH Staff Send Strong Letter Of Dissent To Their Bosses
More than 300 scientists and other staff at the National Institutes of Health sent NIH Director Jay Bhattacharya an unusually strongly worded letter of dissent on Monday.
www.forbes.com
June 9, 2025 at 8:04 PM
Forbes: 'Hundreds Of NIH Staff Send Strong Letter Of Dissent To Their Bosses'
'In addition to Bhattacharya, the letter was sent to U.S. Health and Human Services Secretary Robert F. Kennedy Jr. and members of Congress who oversee NIH'
www.forbes.com/sites/michae...
'In addition to Bhattacharya, the letter was sent to U.S. Health and Human Services Secretary Robert F. Kennedy Jr. and members of Congress who oversee NIH'
www.forbes.com/sites/michae...
You may be excited, @mrvollger.bsky.social, but we are even more so! I can't wait to be your colleague!
Very excited to share I’ll be starting my own group at University of Utah in the Department of Human Genetics in the new year! Reach out if you are interested! vollgerlab.com
June 5, 2025 at 8:19 PM
You may be excited, @mrvollger.bsky.social, but we are even more so! I can't wait to be your colleague!
Reposted by Aaron Quinlan (he/him)
If you’ve ever wondered about the statistical significance of differences among mutational signature profiles, check out our new Aggregate Mutation Spectrum Distance (AMSD) preprint co-led by Sam Hart and @alisonfeder.bsky.social with @nalcala.bsky.social www.biorxiv.org/cgi/content/...
A signature-agnostic test for differences between tumor mutation spectra reveals carcinogen and ancestry effects
Mutational signatures contain valuable information about the mutational processes shaping cancer genomes. However, despite dozens of tools to identify signatures in cancer samples, there is not an est...
www.biorxiv.org
May 20, 2025 at 4:58 PM
If you’ve ever wondered about the statistical significance of differences among mutational signature profiles, check out our new Aggregate Mutation Spectrum Distance (AMSD) preprint co-led by Sam Hart and @alisonfeder.bsky.social with @nalcala.bsky.social www.biorxiv.org/cgi/content/...
The symposium will feature rising science stars with research programs in evolutionary genetics and genomics, functional and disease genetics, and computational genomics. This is always a fun, rewarding, and exciting event!
April 28, 2025 at 5:21 PM
The symposium will feature rising science stars with research programs in evolutionary genetics and genomics, functional and disease genetics, and computational genomics. This is always a fun, rewarding, and exciting event!
We invite postdocs to apply and share their research among a broad group of scientists working in broad areas of genetics and genomics.
April 28, 2025 at 5:21 PM
We invite postdocs to apply and share their research among a broad group of scientists working in broad areas of genetics and genomics.
The Department of Human Genetics at the University of Utah is sponsoring the Rising Stars in Genetics and Genomics symposium!
- We are seeking nominations bu June 1.
- September 18-19, 2025
- Please share with the star postdocs that you know.
docs.google.com/forms/d/e/1F...
- We are seeking nominations bu June 1.
- September 18-19, 2025
- Please share with the star postdocs that you know.
docs.google.com/forms/d/e/1F...
April 28, 2025 at 5:20 PM
The Department of Human Genetics at the University of Utah is sponsoring the Rising Stars in Genetics and Genomics symposium!
- We are seeking nominations bu June 1.
- September 18-19, 2025
- Please share with the star postdocs that you know.
docs.google.com/forms/d/e/1F...
- We are seeking nominations bu June 1.
- September 18-19, 2025
- Please share with the star postdocs that you know.
docs.google.com/forms/d/e/1F...
Biology of Genomes is only 18 days away. The lineup is stellar!
meetings.cshl.edu/meetings.asp...
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
April 18, 2025 at 7:21 PM
Biology of Genomes is only 18 days away. The lineup is stellar!
meetings.cshl.edu/meetings.asp...
meetings.cshl.edu/meetings.asp...
Thank you, Bruce!
April 18, 2025 at 2:09 PM
Thank you, Bruce!
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
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
March 26, 2025 at 7:18 PM
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
Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci."
strchive.org